#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_ ensembl_gene_id	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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP	i_default_gene_name	i_deletion_substructures	i_domain	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_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
CEBPE	1053	genome.wustl.edu	37	14	23586911	23586911	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr14:23586911G>A	ENST00000206513.5	-	2	1155	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W		NM_001805.3	NP_001796.2	Q15744	CEBPE_HUMAN	CCAAT/enhancer binding protein (C/EBP), epsilon	211	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular response to lipopolysaccharide (GO:0071222)|cytokine biosynthetic process (GO:0042089)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|macrophage differentiation (GO:0030225)|phagocytosis (GO:0006909)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0064)		TTGCGCTCCCGCCTCAGCCGG	0.617													ENSG00000092067																									NSCLC(63;1230 1818 14565 22565)												0													64.0	63.0	63.0					14																	23586911		2203	4300	6503	SO:0001583	missense	0			-		CCDS9589.1	14q11.2	2014-09-17			ENSG00000092067	ENSG00000092067		"""basic leucine zipper proteins"""	1836	protein-coding gene	gene with protein product		600749				8661101	Standard	NM_001805		Approved	CRP1	uc001wiv.2	Q15744	OTTHUMG00000028719	ENST00000206513.5:c.631C>T	14.37:g.23586911G>A	ENSP00000206513:p.Arg211Trp		Q15745|Q8IYI2|Q99803	Missense_Mutation	SNP	pfam_bZIP,smart_bZIP,pirsf_CCAAT/enhancer-binding,pfscan_bZIP	p.R211W	ENST00000206513.5	37	c.631	CCDS9589.1	14	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271216	0.80469	.	.	ENSG00000092067	ENST00000206513	T	0.71934	-0.61	5.2	3.19	0.36642	Basic-leucine zipper (bZIP) transcription factor (2);Basic leucine zipper (1);	0.000000	0.85682	D	0.000000	D	0.87947	0.6306	H	0.96301	3.8	0.58432	D	0.999993	D	0.89917	1.0	D	0.91635	0.999	D	0.90741	0.4650	10	0.87932	D	0	-20.5285	12.485	0.55868	0.0:0.0:0.6971:0.3029	.	211	Q15744	CEBPE_HUMAN	W	211	ENSP00000206513:R211W	ENSP00000206513:R211W	R	-	1	2	CEBPE	22656751	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.937000	0.28951	1.137000	0.42214	0.655000	0.94253	CGG	-	CEBPE	-	pfam_bZIP,smart_bZIP,pirsf_CCAAT/enhancer-binding,pfscan_bZIP		0.617	CEBPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CEBPE	HGNC	protein_coding	OTTHUMT00000071716.2	0	0	0	62	62	60	0.00	0.00	G	NM_001805		23586911	-1	65	20	61	27	tier1	no_errors	ENST00000206513	ensembl	human	known	74_37	missense	50.39	42.55	SNP	1.000	A	65	61
SLC22A17	51310	genome.wustl.edu	37	14	23818512	23818512	+	Silent	SNP	A	A	G			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr14:23818512A>G	ENST00000206544.8	-	3	831	c.495T>C	c.(493-495)ctT>ctC	p.L165L	SLC22A17_ENST00000397267.1_Silent_p.L165L|SLC22A17_ENST00000397260.3_Silent_p.L54L|SLC22A17_ENST00000354772.3_Silent_p.L165L|SLC22A17_ENST00000474057.1_5'UTR	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	165					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CAACACCGGCAAGCAGAAAGC	0.627													ENSG00000092096																																					0													67.0	61.0	63.0					14																	23818512		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"""Solute carriers"""	23095	protein-coding gene	gene with protein product	"""neutrophil gelatinase-associated lipocalin receptor"""	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.495T>C	14.37:g.23818512A>G			A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Silent	SNP	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom	p.L165	ENST00000206544.8	37	c.495	CCDS9593.1	14																																																																																			-	SLC22A17	-	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom		0.627	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SLC22A17	HGNC	protein_coding	OTTHUMT00000157223.3	0	0	0	20	20	63	0.00	0.00	A	NM_020372		23818512	-1	22	16	15	23	tier1	no_errors	ENST00000206544	ensembl	human	known	74_37	silent	59.46	41.03	SNP	0.952	G	22	15
TPCN2	219931	genome.wustl.edu	37	11	68839473	68839473	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr11:68839473G>A	ENST00000294309.3	+	11	1144	c.1043G>A	c.(1042-1044)gGa>gAa	p.G348E	TPCN2_ENST00000542467.1_Missense_Mutation_p.G348E|TPCN2_ENST00000442692.2_3'UTR	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	348					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GTGGGGGAGGGAGGAGCCTTC	0.627													ENSG00000162341																																					0													52.0	56.0	54.0					11																	68839473		2200	4294	6494	SO:0001583	missense	0			-	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1043G>A	11.37:g.68839473G>A	ENSP00000294309:p.Gly348Glu		Q9NT82	Missense_Mutation	SNP	pfam_Ion_trans_dom	p.G348E	ENST00000294309.3	37	c.1043	CCDS8189.1	11	.	.	.	.	.	.	.	.	.	.	G	4.184	0.032846	0.08101	.	.	ENSG00000162341	ENST00000356782;ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.97041	-4.22;-4.22	4.27	-3.25	0.05079	.	1.589960	0.03662	N	0.242756	D	0.94235	0.8149	L	0.56769	1.78	0.09310	N	1	B;B;B	0.18741	0.018;0.002;0.03	B;B;B	0.13407	0.008;0.002;0.009	D	0.84221	0.0461	10	0.18710	T	0.47	0.506	6.5814	0.22596	0.3021:0.4946:0.2033:0.0	.	348;348;263	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	E	278;348;263;348	ENSP00000294309:G348E;ENSP00000445551:G348E	ENSP00000294309:G348E	G	+	2	0	TPCN2	68596049	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.578000	0.05841	-0.373000	0.07979	-1.263000	0.01449	GGA	-	TPCN2	-	NULL		0.627	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPCN2	HGNC	protein_coding	OTTHUMT00000396878.2	0	0	0	31	31	64	0.00	0.00	G	NM_139075		68839473	+1	25	29	28	34	tier1	no_errors	ENST00000294309	ensembl	human	known	74_37	missense	47.17	46.03	SNP	0.000	A	25	28
OBSCN	84033	genome.wustl.edu	37	1	228520994	228520994	+	Missense_Mutation	SNP	C	C	T	rs564170262		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr1:228520994C>T	ENST00000422127.1	+	58	15870	c.15826C>T	c.(15826-15828)Cgc>Tgc	p.R5276C	OBSCN_ENST00000284548.11_Missense_Mutation_p.R5276C|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2910C|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6233C|OBSCN_ENST00000366709.4_Missense_Mutation_p.R2395C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5276	Ig-like 50.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCCTGGCACACGCCTGGCCAA	0.637													ENSG00000154358	C|||	1	0.000199681	0.0	0.0	5008	,	,		17603	0.001		0.0	False		,,,				2504	0.0																0													11.0	14.0	13.0					1																	228520994		1999	4132	6131	SO:0001583	missense	0			-	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15826C>T	1.37:g.228520994C>T	ENSP00000409493:p.Arg5276Cys		Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Fibronectin_type3,pfam_DH-domain,pfam_IQ_motif_EF-hand-BS,superfamily_Kinase-like_dom,superfamily_DH-domain,superfamily_Fibronectin_type3,superfamily_SH3_domain,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_IQ_motif_EF-hand-BS,smart_DH-domain,smart_Pleckstrin_homology,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_IQ_motif_EF-hand-BS,pfscan_Pleckstrin_homology,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom,pfscan_DH-domain	p.R5276C	ENST00000422127.1	37	c.15826	CCDS58065.1	1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.958704	0.92726	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.29	5.29	0.74685	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.149514	0.43579	D	0.000550	T	0.60483	0.2272	M	0.74467	2.265	0.44366	D	0.99726	D;D	0.76494	0.999;0.998	P;P	0.60609	0.877;0.804	T	0.61535	-0.7043	10	0.51188	T	0.08	.	14.3599	0.66764	0.0:0.9273:0.0:0.0727	.	5276;5276	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	5276;5276;2910;2395	ENSP00000284548:R5276C;ENSP00000409493:R5276C;ENSP00000355668:R2910C;ENSP00000355670:R2395C	ENSP00000284548:R5276C	R	+	1	0	OBSCN	226587617	0.528000	0.26314	1.000000	0.80357	0.972000	0.66771	2.567000	0.45956	2.745000	0.94114	0.561000	0.74099	CGC	-	OBSCN	-	pfam_Ig_I-set,smart_Ig_sub2,pfscan_Ig-like_dom		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	OBSCN	HGNC	protein_coding		0	0	0	48	48	21	0.00	0.00	C	NM_052843		228520994	+1	28	13	52	18	tier1	no_errors	ENST00000422127	ensembl	human	known	74_37	missense	35.00	41.94	SNP	0.995	T	28	52
KIAA1109	84162	genome.wustl.edu	37	4	123175371	123175371	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr4:123175371G>A	ENST00000264501.4	+	38	6317	c.5944G>A	c.(5944-5946)Gat>Aat	p.D1982N	KIAA1109_ENST00000455637.1_Missense_Mutation_p.D1982N|KIAA1109_ENST00000388738.3_Missense_Mutation_p.D1982N			Q2LD37	K1109_HUMAN	KIAA1109	1982					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CGAATCTGATGATTTGAAAAA	0.368													ENSG00000138688																																					0													119.0	107.0	111.0					4																	123175371		1850	4087	5937	SO:0001583	missense	0			-	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5944G>A	4.37:g.123175371G>A	ENSP00000264501:p.Asp1982Asn		Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	pfam_Fragile_site-assoc_C	p.D1982N	ENST00000264501.4	37	c.5944	CCDS43267.1	4	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.56|17.56	3.418879|3.418879	0.62622|0.62622	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.24350|.	2.45;2.45;1.86|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.000000|.	0.52532|.	U|.	0.000080|.	T|T	0.68081|0.68081	0.2962|0.2962	L|L	0.44542|0.44542	1.39|1.39	0.58432|0.58432	D|D	0.999995|0.999995	D;D|.	0.67145|.	0.996;0.993|.	D;D|.	0.79784|.	0.993;0.984|.	T|T	0.63950|0.63950	-0.6521|-0.6521	10|5	0.15066|.	T|.	0.55|.	.|.	19.0871|19.0871	0.93209|0.93209	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1981;1982|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	N|I	1982|554	ENSP00000264501:D1982N;ENSP00000373390:D1982N;ENSP00000389925:D1982N|.	ENSP00000264501:D1982N|.	D|M	+|+	1|3	0|0	KIAA1109|KIAA1109	123394821|123394821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.787000|9.787000	0.99055|0.99055	2.514000|2.514000	0.84764|0.84764	0.591000|0.591000	0.81541|0.81541	GAT|ATG	-	KIAA1109	-	NULL		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1109	HGNC	protein_coding	OTTHUMT00000316415.1	0	0	0	53	53	55	0.00	0.00	G	NM_020797		123175371	+1	7	5	43	33	tier1	no_errors	ENST00000264501	ensembl	human	known	74_37	missense	14.00	13.16	SNP	1.000	A	7	43
MAP4K5	11183	genome.wustl.edu	37	14	50952895	50952895	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr14:50952895T>C	ENST00000013125.4	-	4	502	c.184A>G	c.(184-186)Att>Gtt	p.I62V	MAP4K5_ENST00000557578.1_5'Flank	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	62	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					TCTTGTTGAATCAAAGAAAAA	0.284													ENSG00000012983																																					0													58.0	53.0	54.0					14																	50952895		1781	3979	5760	SO:0001583	missense	0			-	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.184A>G	14.37:g.50952895T>C	ENSP00000013125:p.Ile62Val		Q8IYF6	Missense_Mutation	SNP	pfam_Citron,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_Citron,pfscan_Prot_kinase_dom	p.I62V	ENST00000013125.4	37	c.184		14	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321213	0.41096	.	.	ENSG00000012983	ENST00000013125;ENST00000557390	T;T	0.65549	-0.16;1.86	5.26	5.26	0.73747	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	0.66167	0.2762	N	0.17674	0.51	0.80722	D	1	B;D	0.53151	0.136;0.958	B;D	0.70716	0.173;0.97	T	0.67776	-0.5583	10	0.41790	T	0.15	.	14.8269	0.70120	0.0:0.0:0.0:1.0	.	62;62	B2R928;Q9Y4K4	.;M4K5_HUMAN	V	62	ENSP00000013125:I62V;ENSP00000451980:I62V	ENSP00000013125:I62V	I	-	1	0	MAP4K5	50022645	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.473000	0.60196	1.998000	0.58463	0.482000	0.46254	ATT	-	MAP4K5	-	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.284	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	MAP4K5	HGNC	protein_coding	OTTHUMT00000410880.1	0	0	0	23	23	80	0.00	0.00	T	NM_006575		50952895	-1	16	32	32	57	tier1	no_errors	ENST00000013125	ensembl	human	known	74_37	missense	33.33	35.96	SNP	1.000	C	16	32
DAK	26007	genome.wustl.edu	37	11	61113888	61113888	+	Silent	SNP	C	C	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr11:61113888C>T	ENST00000394900.3	+	18	1870	c.1641C>T	c.(1639-1641)atC>atT	p.I547I	CYB561A3_ENST00000540317.1_5'Flank	NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	547	DhaL. {ECO:0000255|PROSITE- ProRule:PRU00813}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						CCAGTTATATCAGCTCAGCAC	0.632													ENSG00000149476																																					0													71.0	83.0	79.0					11																	61113888		2203	4299	6502	SO:0001819	synonymous_variant	0			-		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"""dihydroxyacetone kinase 2 homolog (yeast)"""				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1641C>T	11.37:g.61113888C>T			Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Silent	SNP	pfam_Dak1,pfam_DhaL_dom,superfamily_DhaL_dom,tigrfam_DhaK_ATP	p.I547	ENST00000394900.3	37	c.1641	CCDS8003.1	11																																																																																			-	DAK	-	pfam_DhaL_dom,superfamily_DhaL_dom,tigrfam_DhaK_ATP		0.632	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DAK	HGNC	protein_coding	OTTHUMT00000394425.4	0	0	0	22	22	17	0.00	0.00	C	NM_015533		61113888	+1	23	6	23	11	tier1	no_errors	ENST00000394900	ensembl	human	known	74_37	silent	50.00	35.29	SNP	1.000	T	23	23
WRAP53	55135	genome.wustl.edu	37	17	7592319	7592319	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr17:7592319C>T	ENST00000316024.5	+	1	2701	c.353C>T	c.(352-354)gCg>gTg	p.A118V	TP53_ENST00000455263.2_5'Flank|WRAP53_ENST00000534050.1_Missense_Mutation_p.A118V|WRAP53_ENST00000396463.2_Missense_Mutation_p.A118V|TP53_ENST00000420246.2_5'Flank|TP53_ENST00000445888.2_5'Flank|WRAP53_ENST00000431639.2_Missense_Mutation_p.A118V|TP53_ENST00000269305.4_5'Flank|RP11-199F11.2_ENST00000571370.1_RNA|WRAP53_ENST00000457584.2_Missense_Mutation_p.A118V			Q9BUR4	WAP53_HUMAN	WD repeat containing, antisense to TP53	118					positive regulation of telomerase activity (GO:0051973)|telomere formation via telomerase (GO:0032203)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(2)	18						GAAGAAGAAGCGAACGGGCCA	0.532													ENSG00000141499																																					0													68.0	77.0	74.0					17																	7592319		2203	4300	6503	SO:0001583	missense	0			-	AK001247, DQ431240	CCDS11119.1	17p13.1	2014-09-17	2009-02-16	2009-02-16	ENSG00000141499	ENSG00000141499		"""WD repeat domain containing"""	25522	protein-coding gene	gene with protein product	"""telomerase cajal body protein 1"", ""WD-encoding RNA antisense to p53"""	612661	"""WD repeat domain 79"""	WDR79		19179534, 19250907, 19571673, 19342896, 20494116, 21441950	Standard	NM_018081		Approved	FLJ10385, TCAB1	uc010vuh.2	Q9BUR4	OTTHUMG00000134323	ENST00000316024.5:c.353C>T	17.37:g.7592319C>T	ENSP00000324203:p.Ala118Val		B3KPR9|D3DTQ4|Q08ET9|Q9NW09	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.A118V	ENST00000316024.5	37	c.353	CCDS11119.1	17	.	.	.	.	.	.	.	.	.	.	C	12.53	1.966460	0.34659	.	.	ENSG00000141499	ENST00000431639;ENST00000316024;ENST00000457584;ENST00000396463;ENST00000534050	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.78	5.41	0.942	0.19525	.	0.922668	0.09125	N	0.845143	T	0.23926	0.0579	N	0.03608	-0.345	0.09310	N	1	B;B	0.21147	0.0;0.052	B;B	0.12156	0.0;0.007	T	0.22661	-1.0210	10	0.15499	T	0.54	.	5.4443	0.16527	0.0:0.4808:0.3396:0.1795	.	118;118	E9PMG4;Q9BUR4	.;WAP53_HUMAN	V	118	ENSP00000397219:A118V;ENSP00000324203:A118V;ENSP00000411061:A118V;ENSP00000379727:A118V;ENSP00000434999:A118V	ENSP00000324203:A118V	A	+	2	0	WRAP53	7533044	0.001000	0.12720	0.014000	0.15608	0.124000	0.20399	-1.589000	0.02104	0.403000	0.25479	-0.244000	0.11960	GCG	-	WRAP53	-	NULL		0.532	WRAP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WRAP53	HGNC	protein_coding	OTTHUMT00000259385.2	0	0	0	19	19	88	0.00	0.00	C	NM_018081		7592319	+1	48	108	2	15	tier1	no_errors	ENST00000316024	ensembl	human	known	74_37	missense	96.00	85.71	SNP	0.000	T	48	2
LPP	4026	genome.wustl.edu	37	3	187896990	187896990	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr3:187896990T>C	ENST00000392468.2	+	1	660	c.19T>C	c.(19-21)Ttt>Ctt	p.F7L	LPP_ENST00000448637.1_Intron																kidney(1)	1						CTCCAAGGCTTTTGAATTTGC	0.522													ENSG00000213132																																					0													53.0	48.0	49.0					3																	187896990		692	1591	2283	SO:0001583	missense	0			-																												ENST00000392468.2:c.19T>C	3.37:g.187896990T>C	ENSP00000376261:p.Phe7Leu			Missense_Mutation	SNP	NULL	p.F7L	ENST00000392468.2	37	c.19		3	.	.	.	.	.	.	.	.	.	.	T	10.49	1.365362	0.24684	.	.	ENSG00000213132	ENST00000392468	.	.	.	4.02	1.66	0.24008	.	.	.	.	.	T	0.39436	0.1078	.	.	.	0.20074	N	0.999932	.	.	.	.	.	.	T	0.35649	-0.9780	5	0.87932	D	0	.	5.4247	0.16419	0.0:0.229:0.0:0.771	.	.	.	.	L	7	.	ENSP00000376261:F7L	F	+	1	0	AC022498.1	189379684	0.023000	0.18921	0.007000	0.13788	0.011000	0.07611	0.490000	0.22403	0.375000	0.24679	0.459000	0.35465	TTT	-	AC022498.1	-	NULL		0.522	AC022498.1-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000213132	Clone_based_ensembl_gene	protein_coding		0	0	0	30	30	62	0.00	0.00	T			187896990	+1	24	21	24	24	tier1	no_errors	ENST00000392468	ensembl	human	known	74_37	missense	50.00	46.67	SNP	0.010	C	24	24
DMD	1756	genome.wustl.edu	37	X	31515003	31515003	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chrX:31515003G>A	ENST00000357033.4	-	57	8655	c.8449C>T	c.(8449-8451)Ctt>Ttt	p.L2817F	DMD_ENST00000445312.1_5'UTR|DMD_ENST00000378707.3_Missense_Mutation_p.L357F|DMD_ENST00000359836.1_Missense_Mutation_p.L357F|DMD_ENST00000343523.2_Missense_Mutation_p.L357F|DMD_ENST00000541735.1_Missense_Mutation_p.L357F|DMD_ENST00000474231.1_Missense_Mutation_p.L357F|DMD_ENST00000378677.2_Missense_Mutation_p.L2813F	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2817					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CACACCAGAAGTTCCTGCAGA	0.488													ENSG00000198947																																					0													64.0	50.0	55.0					X																	31515003		2202	4300	6502	SO:0001583	missense	0			-	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8449C>T	X.37:g.31515003G>A	ENSP00000354923:p.Leu2817Phe		E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	pfam_Spectrin_repeat,pfam_EF-hand_dom_typ1,pfam_EF-hand_dom_typ2,pfam_CH-domain,pfam_Znf_ZZ,pfam_WW_dom,pfam_CAMSAP_CH,superfamily_CH-domain,superfamily_WW_dom,smart_CH-domain,smart_Spectrin/alpha-actinin,smart_WW_dom,smart_Znf_ZZ,pirsf_Dystrophin/utrophin,pfscan_CH-domain,pfscan_WW_dom,pfscan_Znf_ZZ	p.L2817F	ENST00000357033.4	37	c.8449	CCDS14233.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.5|23.5	4.426941|4.426941	0.83667|0.83667	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231|ENST00000465285	T;T;T;T;T;T;T;T|.	0.42131|.	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	0.000000|.	0.33712|.	U|.	0.004637|.	T|T	0.72045|0.72045	0.3412|0.3412	L|L	0.55103|0.55103	1.725|1.725	0.54753|0.54753	D|D	0.999982|0.999982	P;P;D;P;P;P;P;P;B;P;D|.	0.71674|.	0.947;0.911;0.998;0.911;0.911;0.937;0.598;0.598;0.355;0.487;0.994|.	P;P;D;B;B;P;B;B;B;B;D|.	0.78314|.	0.901;0.532;0.991;0.402;0.402;0.742;0.325;0.325;0.092;0.189;0.943|.	T|T	0.68300|0.68300	-0.5445|-0.5445	10|5	0.66056|.	D|.	0.02|.	.|.	19.1264|19.1264	0.93386|0.93386	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2809;2817;2813;1476;1473;357;357;357;357;357;2694|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3|.	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.|.	F|I	2809;1476;1473;513;2813;2817;357;357;2817;2694;357;357;357|545	ENSP00000350765:L513F;ENSP00000367948:L2813F;ENSP00000354923:L2817F;ENSP00000352894:L357F;ENSP00000340057:L357F;ENSP00000367979:L357F;ENSP00000444119:L357F;ENSP00000417123:L357F|.	ENSP00000340057:L357F|.	L|T	-|-	1|2	0|0	DMD|DMD	31424924|31424924	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.963000|0.963000	0.63663|0.63663	7.920000|7.920000	0.87521|0.87521	2.466000|2.466000	0.83321|0.83321	0.594000|0.594000	0.82650|0.82650	CTT|ACT	-	DMD	-	smart_Spectrin/alpha-actinin,pirsf_Dystrophin/utrophin		0.488	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DMD	HGNC	protein_coding	OTTHUMT00000056182.2	0	0	0	35	35	80	0.00	0.00	G	NM_004006		31515003	-1	26	32	32	43	tier1	no_errors	ENST00000357033	ensembl	human	known	74_37	missense	44.83	42.67	SNP	1.000	A	26	32
PRDM2	7799	genome.wustl.edu	37	1	14106018	14106018	+	Silent	SNP	T	T	G			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr1:14106018T>G	ENST00000235372.7	+	8	2584	c.1728T>G	c.(1726-1728)acT>acG	p.T576T	PRDM2_ENST00000343137.4_Silent_p.T375T|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000311066.5_Silent_p.T576T|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Silent_p.T375T	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	576					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AAATTCAAACTAATAACAACA	0.373													ENSG00000116731																																					0													48.0	51.0	50.0					1																	14106018		2203	4300	6503	SO:0001819	synonymous_variant	0			-	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.1728T>G	1.37:g.14106018T>G			B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	pfam_SET_dom,smart_SET_dom,smart_Znf_C2H2-like,pirsf_RIZ_retinblastoma-bd_prot,pfscan_SET_dom,pfscan_Znf_C2H2	p.T576	ENST00000235372.7	37	c.1728	CCDS150.1	1																																																																																			-	PRDM2	-	pirsf_RIZ_retinblastoma-bd_prot		0.373	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRDM2	HGNC	protein_coding	OTTHUMT00000021792.2	0	0	0	25	25	61	0.00	0.00	T	NM_012231		14106018	+1	22	27	26	52	tier1	no_errors	ENST00000235372	ensembl	human	known	74_37	silent	45.83	34.18	SNP	1.000	G	22	26
SCN2A	6326	genome.wustl.edu	37	2	166245346	166245346	+	Missense_Mutation	SNP	T	T	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr2:166245346T>A	ENST00000375437.2	+	27	5320	c.5030T>A	c.(5029-5031)tTt>tAt	p.F1677Y	SCN2A_ENST00000283256.6_Missense_Mutation_p.F1677Y|SCN2A_ENST00000357398.3_Missense_Mutation_p.F1677Y|SCN2A_ENST00000375427.2_Missense_Mutation_p.F1677Y	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1677					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TACGCCATCTTTGGGATGTCC	0.463													ENSG00000136531																																					0													191.0	181.0	184.0					2																	166245346		2203	4300	6503	SO:0001583	missense	0			-	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5030T>A	2.37:g.166245346T>A	ENSP00000364586:p.Phe1677Tyr		A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_Na_trans_assoc,pfam_DUF3451,pfam_PKD1_2_channel,smart_IQ_motif_EF-hand-BS,prints_Na_channel_asu,prints_PKD_2,pfscan_IQ_motif_EF-hand-BS	p.F1677Y	ENST00000375437.2	37	c.5030	CCDS33314.1	2	.	.	.	.	.	.	.	.	.	.	T	18.63	3.665056	0.67700	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03	5.5	5.5	0.81552	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99272	0.9746	M	0.91140	3.18	0.58432	D	0.999999	D;P	0.69078	0.997;0.801	D;P	0.72982	0.979;0.797	D	0.99087	1.0839	10	0.87932	D	0	.	15.9562	0.79889	0.0:0.0:0.0:1.0	.	1677;1677	Q99250-2;Q99250	.;SCN2A_HUMAN	Y	1677	ENSP00000364586:F1677Y;ENSP00000349973:F1677Y;ENSP00000283256:F1677Y;ENSP00000364576:F1677Y	ENSP00000283256:F1677Y	F	+	2	0	SCN2A	165953592	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.994000	0.88315	2.227000	0.72691	0.524000	0.50904	TTT	-	SCN2A	-	pfam_Ion_trans_dom,pfam_PKD1_2_channel		0.463	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SCN2A	HGNC	protein_coding	OTTHUMT00000102659.2	0	0	0	83	83	62	0.00	0.00	T	NM_021007		166245346	+1	114	52	121	60	tier1	no_errors	ENST00000283256	ensembl	human	known	74_37	missense	48.51	46.43	SNP	1.000	A	114	121
CFH	3075	genome.wustl.edu	37	1	196695646	196695646	+	Silent	SNP	T	T	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr1:196695646T>C	ENST00000367429.4	+	13	2160	c.1920T>C	c.(1918-1920)aaT>aaC	p.N640N		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	640	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TCAATGGGAATGTTAAGGAAA	0.328													ENSG00000000971																																					0													80.0	86.0	84.0					1																	196695646		2203	4299	6502	SO:0001819	synonymous_variant	0			-	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.1920T>C	1.37:g.196695646T>C			A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP	p.N640	ENST00000367429.4	37	c.1920	CCDS1385.1	1																																																																																			-	CFH	-	pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP		0.328	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CFH	HGNC	protein_coding	OTTHUMT00000086412.2	0	0	0	34	34	93	0.00	0.00	T	NM_000186		196695646	+1	16	30	21	53	tier1	no_errors	ENST00000367429	ensembl	human	known	74_37	silent	43.24	36.14	SNP	0.000	C	16	21
GPRIN1	114787	genome.wustl.edu	37	5	176025351	176025351	+	Silent	SNP	G	G	A	rs147157849		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr5:176025351G>A	ENST00000303991.4	-	2	1662	c.1485C>T	c.(1483-1485)ggC>ggT	p.G495G		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	495					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACCTGGGATCGCCTGGACCTG	0.552													ENSG00000169258	g|||	1	0.000199681	0.0	0.0	5008	,	,		20728	0.001		0.0	False		,,,				2504	0.0																0													82.0	91.0	88.0					5																	176025351		2203	4294	6497	SO:0001819	synonymous_variant	0			GMAF=0.0005	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1485C>T	5.37:g.176025351G>A			C9JM70|Q8ND74|Q96PZ4	Silent	SNP	NULL	p.G495	ENST00000303991.4	37	c.1485	CCDS4405.1	5																																																																																			rs147157849	GPRIN1	-	NULL		0.552	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPRIN1	HGNC	protein_coding	OTTHUMT00000253149.1	0	0	0	26	26	111	0.00	0.00	G	NM_052899		176025351	-1	13	34	13	64	tier1	no_errors	ENST00000303991	ensembl	human	known	74_37	silent	48.15	34.34	SNP	0.000	A	13	13
RTFDC1	51507	genome.wustl.edu	37	20	55093355	55093355	+	3'UTR	SNP	T	T	G			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr20:55093355T>G	ENST00000023939.4	+	0	1062				GCNT7_ENST00000243913.4_Intron|RTFDC1_ENST00000357348.5_3'UTR|RTFDC1_ENST00000395881.3_3'UTR|FAM209A_ENST00000481560.1_Splice_Site	NM_001283035.1|NM_001283036.1|NM_016407.3	NP_001269964.1|NP_001269965.1|NP_057491.2	Q9BY42	RTF2_HUMAN	replication termination factor 2 domain containing 1																		CCCCAGAAGGTTGTTTAGTTT	0.582													ENSG00000124103																																					0													43.0	47.0	46.0					20																	55093355		2203	4300	6503	SO:0001624	3_prime_UTR_variant	0			-	AF161513	CCDS13453.1, CCDS63316.1, CCDS63317.1	20q13	2012-10-29	2012-10-29	2012-10-29	ENSG00000022277	ENSG00000022277			15890	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 43"""	C20orf43			Standard	NM_001283035		Approved	HSPC164, CDAO5	uc002xxt.2	Q9BY42	OTTHUMG00000032801	ENST00000023939.4:c.*34T>G	20.37:g.55093355T>G			E1P5Z9|Q9BYL7|Q9HCV9|Q9NX29|Q9NZZ8|Q9P002|Q9UHW3	Splice_Site	SNP	-	NULL	ENST00000023939.4	37	c.NULL	CCDS13453.1	20																																																																																			-	FAM209A	-	-		0.582	RTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM209A	HGNC	protein_coding	OTTHUMT00000079817.2	0	0	0	15	15	91	0.00	0.00	T	NM_016407		55093355	+1	21	26	17	42	tier1	no_errors	ENST00000481560	ensembl	human	known	74_37	splice_site	55.26	38.24	SNP	0.000	G	21	17
ARHGEF6	9459	genome.wustl.edu	37	X	135827388	135827388	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chrX:135827388C>A	ENST00000250617.6	-	4	1658	c.453G>T	c.(451-453)aaG>aaT	p.K151N	ARHGEF6_ENST00000370622.1_5'UTR|ARHGEF6_ENST00000370620.1_5'UTR|ARHGEF6_ENST00000535227.1_5'UTR	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	151					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TTACCACTGTCTTTGACTGCC	0.438													ENSG00000129675																																					0													231.0	210.0	217.0					X																	135827388		2203	4300	6503	SO:0001583	missense	0			-	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.453G>T	X.37:g.135827388C>A	ENSP00000250617:p.Lys151Asn		A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	pfam_DH-domain,pfam_SH3_2,pfam_SH3_domain,pfam_CH-domain,pfam_Pleckstrin_homology,pfam_CAMSAP_CH,superfamily_DH-domain,superfamily_CH-domain,superfamily_SH3_domain,smart_CH-domain,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_CH-domain,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain,prints_SH3_domain,prints_SM22_calponin	p.K151N	ENST00000250617.6	37	c.453	CCDS14660.1	X	.	.	.	.	.	.	.	.	.	.	C	15.71	2.912946	0.52439	.	.	ENSG00000129675	ENST00000250617	T	0.56275	0.47	5.15	4.28	0.50868	Src homology-3 domain (1);	0.142157	0.64402	D	0.000007	T	0.54111	0.1838	L	0.55481	1.735	0.80722	D	1	P	0.48640	0.913	P	0.50352	0.638	T	0.57081	-0.7872	10	0.59425	D	0.04	.	8.4248	0.32723	0.0:0.7562:0.0:0.2438	.	151	Q15052	ARHG6_HUMAN	N	151	ENSP00000250617:K151N	ENSP00000250617:K151N	K	-	3	2	ARHGEF6	135655054	0.971000	0.33674	0.995000	0.50966	0.952000	0.60782	1.494000	0.35616	2.145000	0.66743	0.529000	0.55759	AAG	-	ARHGEF6	-	superfamily_SH3_domain		0.438	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF6	HGNC	protein_coding	OTTHUMT00000058511.2	0	0	0	26	26	137	0.00	0.00	C	NM_004840		135827388	-1	14	16	63	96	tier1	no_errors	ENST00000250617	ensembl	human	known	74_37	missense	18.18	14.29	SNP	0.996	A	14	63
SNHG14	104472715	genome.wustl.edu	37	15	25287085	25287085	+	RNA	SNP	T	T	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr15:25287085T>A	ENST00000552781.1	+	0	328				SNORD109A_ENST00000459128.1_RNA																							TAAGCCTGGCTGTGGAAATGC	0.393													ENSG00000270246																																					0													52.0	51.0	51.0					15																	25287085		876	1991	2867			0			-																													15.37:g.25287085T>A				R	SNP	-	NULL	ENST00000552781.1	37	NULL		15																																																																																			-	SNORD109A	-	-		0.393	RP11-701H24.10-001	KNOWN	basic|readthrough_transcript	processed_transcript	SNORD109A	HGNC	processed_transcript	OTTHUMT00000473258.1	0	0	0	44	44	65	0.00	0.00	T			25287085	+1	47	35	78	47	tier1	no_errors	ENST00000604135	ensembl	human	known	74_37	rna	37.60	42.68	SNP	0.839	A	47	78
GPR137B	7107	genome.wustl.edu	37	1	236343299	236343299	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr1:236343299G>C	ENST00000366592.3	+	4	899	c.808G>C	c.(808-810)Gat>Cat	p.D270H	GPR137B_ENST00000366591.4_Missense_Mutation_p.D179H	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	270						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			CCATTCCTTTGATTATGACTG	0.522													ENSG00000077585																																					0													173.0	145.0	154.0					1																	236343299		2203	4300	6503	SO:0001583	missense	0			-	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"""transmembrane 7 superfamily member 1 (upregulated in kidney)"""	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.808G>C	1.37:g.236343299G>C	ENSP00000355551:p.Asp270His		Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	NULL	p.D270H	ENST00000366592.3	37	c.808	CCDS1609.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.7|25.7	4.666555|4.666555	0.88251|0.88251	.|.	.|.	ENSG00000077585|ENSG00000077585	ENST00000366592;ENST00000366591;ENST00000391852;ENST00000419162|ENST00000454895	T;T;T|.	0.50813|.	0.74;0.73;0.78|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77498|0.77498	0.4139|0.4139	M|M	0.76002|0.76002	2.32|2.32	0.48341|0.48341	D|D	0.99963|0.99963	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.76526|0.76526	-0.2927|-0.2927	10|5	0.87932|.	D|.	0|.	-15.3472|-15.3472	19.5534|19.5534	0.95331|0.95331	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	133;270|.	Q5TAF1;O60478|.	.;G137B_HUMAN|.	H|F	270;179;269;52|133	ENSP00000355551:D270H;ENSP00000355550:D179H;ENSP00000401841:D52H|.	ENSP00000355550:D179H|.	D|L	+|+	1|3	0|2	GPR137B|GPR137B	234409922|234409922	1.000000|1.000000	0.71417|0.71417	0.948000|0.948000	0.38648|0.38648	0.907000|0.907000	0.53573|0.53573	9.292000|9.292000	0.96076|0.96076	2.697000|2.697000	0.92050|0.92050	0.563000|0.563000	0.77884|0.77884	GAT|TTG	-	GPR137B	-	NULL		0.522	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR137B	HGNC	protein_coding	OTTHUMT00000092761.1	0	0	0	22	22	63	0.00	0.00	G	NM_003272		236343299	+1	17	23	19	20	tier1	no_errors	ENST00000366592	ensembl	human	known	74_37	missense	47.22	53.49	SNP	1.000	C	17	19
YES1	7525	genome.wustl.edu	37	18	736829	736829	+	Missense_Mutation	SNP	T	T	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr18:736829T>A	ENST00000584307.1	-	10	1440	c.1270A>T	c.(1270-1272)Aat>Tat	p.N424Y	YES1_ENST00000314574.4_Missense_Mutation_p.N424Y|RP11-769O8.1_ENST00000583314.1_RNA|RP11-769O8.3_ENST00000581712.1_RNA|YES1_ENST00000577961.1_Missense_Mutation_p.N429Y|RP11-769O8.2_ENST00000579595.1_RNA			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	424	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	GTGTATTCATTGTCTTCAATT	0.353													ENSG00000176105																																					0													107.0	93.0	98.0					18																	736829		2202	4298	6500	SO:0001583	missense	0			-	M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"""SH2 domain containing"""	12841	protein-coding gene	gene with protein product		164880	"""v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"""			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.1270A>T	18.37:g.736829T>A	ENSP00000462468:p.Asn424Tyr		A6NLB3|D3DUH1	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH2,pfam_SH3_domain,pfam_SH3_2,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2,prints_SH3_domain	p.N424Y	ENST00000584307.1	37	c.1270	CCDS11824.1	18	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597495	0.87055	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	D	0.83075	-1.68	5.26	5.26	0.73747	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88962	0.6580	M	0.73598	2.24	0.80722	D	1	D	0.55385	0.971	P	0.57244	0.816	D	0.90485	0.4463	10	0.87932	D	0	.	15.4771	0.75489	0.0:0.0:0.0:1.0	.	424	P07947	YES_HUMAN	Y	424	ENSP00000324740:N424Y	ENSP00000324740:N424Y	N	-	1	0	YES1	726829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.194000	0.72082	2.116000	0.64780	0.528000	0.53228	AAT	-	YES1	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.353	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	YES1	HGNC	protein_coding	OTTHUMT00000440827.2	0	0	0	34	34	58	0.00	0.00	T	NM_005433		736829	-1	34	18	26	20	tier1	no_errors	ENST00000314574	ensembl	human	known	74_37	missense	56.67	47.37	SNP	1.000	A	34	26
WRAP53	55135	genome.wustl.edu	37	17	7592045	7592045	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr17:7592045delC	ENST00000316024.5	+	1	2427	c.79delC	c.(79-81)cccfs	p.P27fs	TP53_ENST00000455263.2_5'Flank|WRAP53_ENST00000534050.1_Frame_Shift_Del_p.P27fs|WRAP53_ENST00000396463.2_Frame_Shift_Del_p.P27fs|TP53_ENST00000420246.2_5'Flank|TP53_ENST00000445888.2_5'Flank|WRAP53_ENST00000431639.2_Frame_Shift_Del_p.P27fs|TP53_ENST00000269305.4_5'Flank|RP11-199F11.2_ENST00000571370.1_RNA|WRAP53_ENST00000457584.2_Frame_Shift_Del_p.P27fs			Q9BUR4	WAP53_HUMAN	WD repeat containing, antisense to TP53	27	Pro-rich.				positive regulation of telomerase activity (GO:0051973)|telomere formation via telomerase (GO:0032203)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(2)	18						CCATCCTTCTCCCCACGCTTC	0.592													ENSG00000141499																																					0													67.0	74.0	72.0					17																	7592045		2203	4300	6503	SO:0001589	frameshift_variant	0				AK001247, DQ431240	CCDS11119.1	17p13.1	2014-09-17	2009-02-16	2009-02-16	ENSG00000141499	ENSG00000141499		"""WD repeat domain containing"""	25522	protein-coding gene	gene with protein product	"""telomerase cajal body protein 1"", ""WD-encoding RNA antisense to p53"""	612661	"""WD repeat domain 79"""	WDR79		19179534, 19250907, 19571673, 19342896, 20494116, 21441950	Standard	NM_018081		Approved	FLJ10385, TCAB1	uc010vuh.2	Q9BUR4	OTTHUMG00000134323	ENST00000316024.5:c.79delC	17.37:g.7592045delC	ENSP00000324203:p.Pro27fs		B3KPR9|D3DTQ4|Q08ET9|Q9NW09	Frame_Shift_Del	DEL	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.H28fs	ENST00000316024.5	37	c.79	CCDS11119.1	17																																																																																				WRAP53	-	NULL		0.592	WRAP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WRAP53	HGNC	protein_coding	OTTHUMT00000259385.2	0	0	0	28	28	84	0.00	0.00	C	NM_018081		7592045	+1	267	316	19	43	tier1	no_errors	ENST00000316024	ensembl	human	known	74_37	frame_shift_del	93.36	88.02	DEL	0.345	-	267	19
RB1	5925	genome.wustl.edu	37	13	48954327	48954328	+	Frame_Shift_Del	DEL	AT	AT	-	rs367661403		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	AT	AT	AT	-	AT	AT	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr13:48954327_48954328delAT	ENST00000267163.4	+	16	1586_1587	c.1448_1449delAT	c.(1447-1449)catfs	p.H483fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	483	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.H483fs*9(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AACATTTTTCATATGTCTTTAT	0.238		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			ENSG00000139687																											yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	24	Whole gene deletion(15)|Unknown(8)|Deletion - Frameshift(1)	bone(11)|breast(5)|eye(2)|central_nervous_system(2)|adrenal_gland(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	GRCh37	CI030637|CI071455|CM016043	RB1	I|M																																				SO:0001589	frameshift_variant	0	Familial Cancer Database			M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1448_1449delAT	13.37:g.48954329_48954330delAT	ENSP00000267163:p.His483fs		A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Del	DEL	pfam_RB_C,pfam_RB_A,pfam_RB_B,pfam_RB_N,superfamily_Cyclin-like,smart_Cyclin-like	p.M484fs	ENST00000267163.4	37	c.1448_1449	CCDS31973.1	13																																																																																				RB1	-	pfam_RB_A,superfamily_Cyclin-like		0.238	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	RB1	HGNC	protein_coding	OTTHUMT00000044884.1	0	0	0	33	33	42	0.00	0.00	AT			48954328	+1	25	19	2	10	tier1	no_errors	ENST00000267163	ensembl	human	known	74_37	frame_shift_del	92.59	65.52	DEL	1.000:1.000	-	25	2
CAMKK2	10645	genome.wustl.edu	37	12	121678327	121678328	+	3'UTR	INS	-	-	TTT	rs398056010|rs201965034|rs200501220|rs63023660|rs398021385		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	-	-	-	TTT	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr12:121678327_121678328insTTT	ENST00000324774.5	-	0	2769_2770				CAMKK2_ENST00000337174.3_3'UTR|CAMKK2_ENST00000404169.3_Intron|CAMKK2_ENST00000392474.2_In_Frame_Ins_p.538_539insK|CAMKK2_ENST00000347034.2_3'UTR|CAMKK2_ENST00000412367.2_Intron|CAMKK2_ENST00000545538.1_In_Frame_Ins_p.325_326insK|CAMKK2_ENST00000538733.1_3'UTR	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta						calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GAGTCAAGTCCTTTTTTTTTTT	0.495													ENSG00000110931																																					0																																										SO:0001624	3_prime_UTR_variant	0				AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.*175->AAA	12.37:g.121678334_121678336dupTTT			A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	In_Frame_Ins	INS	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.538in_frame_insK	ENST00000324774.5	37	c.1615_1614	CCDS9216.1	12																																																																																				CAMKK2	-	NULL		0.495	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CAMKK2	HGNC	protein_coding	OTTHUMT00000402563.1	0	0	0	35	35	13	0.00	0.00	-	NM_172226		121678328	-1	7	3	36	23	tier1	no_errors	ENST00000392474	ensembl	human	known	74_37	in_frame_ins	16.28	11.54	INS	0.005:0.000	TTT	7	36
ABCC12	94160	genome.wustl.edu	37	16	48149490	48149490	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr16:48149490G>T	ENST00000311303.3	-	13	2170	c.1825C>A	c.(1825-1827)Cag>Aag	p.Q609K	ABCC12_ENST00000416054.1_Silent_p.G584G|ABCC12_ENST00000448542.1_Missense_Mutation_p.Q609K	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	609	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CTAATCCTCTGCCTCTGCCCC	0.637													ENSG00000140798																																					0													50.0	46.0	48.0					16																	48149490		2201	4300	6501	SO:0001583	missense	0			-	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1825C>A	16.37:g.48149490G>T	ENSP00000311030:p.Gln609Lys		Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_P-loop_NTPase,superfamily_ABC1_TM_dom,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom	p.Q609K	ENST00000311303.3	37	c.1825	CCDS10730.1	16	.	.	.	.	.	.	.	.	.	.	G	25.9	4.684884	0.88639	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	D;D	0.93547	-3.24;-3.24	5.09	5.09	0.68999	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.97090	0.9049	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97690	1.0178	10	0.72032	D	0.01	.	17.6475	0.88152	0.0:0.0:1.0:0.0	.	609	Q96J65	MRP9_HUMAN	K	609;609;551	ENSP00000311030:Q609K;ENSP00000401855:Q609K	ENSP00000311030:Q609K	Q	-	1	0	ABCC12	46706991	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	9.400000	0.97290	2.512000	0.84698	0.563000	0.77884	CAG	-	ABCC12	-	pfam_ABC_transporter-like,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like		0.637	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCC12	HGNC	protein_coding	OTTHUMT00000256837.1	0	0	0	32	32	37	0.00	0.00	G	NM_033226		48149490	-1	6	6	27	9	tier1	no_errors	ENST00000311303	ensembl	human	known	74_37	missense	18.18	40.00	SNP	1.000	T	6	27
GEMIN4	50628	genome.wustl.edu	37	17	656793	656793	+	5'Flank	SNP	T	T	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr17:656793T>C	ENST00000319004.5	-	0	0				GEMIN4_ENST00000437269.1_5'Flank|DBIL5P_ENST00000536214.1_RNA	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4						gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		ATGGCTGAAATGTCCTGAAAC	0.512													ENSG00000231784																																					0																																										SO:0001631	upstream_gene_variant	0			-	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678			17.37:g.656793T>C	Exception_encountered		Q9NZS7|Q9UG32|Q9Y4Q2	R	SNP	-	NULL	ENST00000319004.5	37	NULL	CCDS45559.1	17																																																																																			-	DBIL5P	-	-		0.512	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DBIL5P	HGNC	protein_coding	OTTHUMT00000437181.1	0	0	0	18	18	100	0.00	0.00	T	NM_015721		656793	+1	23	49	1	8	tier1	no_errors	ENST00000536214	ensembl	human	known	74_37	rna	95.83	84.48	SNP	0.000	C	23	1
GLB1L2	89944	genome.wustl.edu	37	11	134241002	134241002	+	Nonsense_Mutation	SNP	C	C	A	rs561326208	byFrequency	TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr11:134241002C>A	ENST00000535456.2	+	13	1504	c.1316C>A	c.(1315-1317)tCg>tAg	p.S439*	GLB1L2_ENST00000339772.7_Nonsense_Mutation_p.S439*|GLB1L2_ENST00000389881.3_Nonsense_Mutation_p.S439*|GLB1L2_ENST00000529077.1_3'UTR	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	439					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		AGCATCACCTCGTCTGGCATC	0.527													ENSG00000149328																																					0													139.0	132.0	134.0					11																	134241002		2201	4297	6498	SO:0001587	stop_gained	0			-		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1316C>A	11.37:g.134241002C>A	ENSP00000444628:p.Ser439*		A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Nonsense_Mutation	SNP	pfam_Glycoside_Hdrlase_35,pfam_Glyco_hydro_42_N,superfamily_Glycoside_hydrolase_SF,superfamily_Galactose-bd-like,prints_Glycoside_Hdrlase_35	p.S439*	ENST00000535456.2	37	c.1316	CCDS31724.1	11	.	.	.	.	.	.	.	.	.	.	C	16.79	3.219224	0.58560	.	.	ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881	.	.	.	5.77	1.54	0.23209	.	0.791393	0.11785	N	0.529800	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-0.806	7.9231	0.29859	0.4021:0.372:0.2259:0.0	.	.	.	.	X	439	.	ENSP00000344659:S439X	S	+	2	0	GLB1L2	133746212	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.513000	0.22770	0.868000	0.35678	-1.014000	0.02459	TCG	-	GLB1L2	-	NULL		0.527	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GLB1L2	HGNC	protein_coding	OTTHUMT00000393629.2	0	0	1	30	30	104	0.00	0.95	C	NM_138342		134241002	+1	23	41	2	3	tier1	no_errors	ENST00000339772	ensembl	human	known	74_37	nonsense	92.00	93.18	SNP	0.000	A	23	2
PKD1	5310	genome.wustl.edu	37	16	2159518	2159520	+	In_Frame_Del	DEL	CCG	CCG	-	rs370043391		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	CCG	CCG	CCG	-	CCG	CCG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr16:2159518_2159520delCCG	ENST00000262304.4	-	15	5856_5858	c.5648_5650delCGG	c.(5647-5652)gcggag>gag	p.A1883del	PKD1_ENST00000423118.1_In_Frame_Del_p.A1883del|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1883	PKD 14. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ATGGGCTCCTCCGCCGTGAGGTT	0.64													ENSG00000008710																																					0																																										SO:0001651	inframe_deletion	0				L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.5648_5650delCGG	16.37:g.2159521_2159523delCCG	ENSP00000262304:p.Ala1883del		Q15140|Q15141	In_Frame_Del	DEL	pfam_PKD_dom,pfam_PKD1_2_channel,pfam_PKD/REJ-like,pfam_PLAT/LH2_dom,pfam_C-type_lectin,pfam_WSC_carb-bd,pfam_GPS_dom,superfamily_C-type_lectin_fold,superfamily_Lipase_LipOase,superfamily_PKD_dom,superfamily_Fe_hydrogenase,smart_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_WSC_carb-bd_subgr,smart_PKD/Chitinase_dom,smart_C-type_lectin,smart_GPS_dom,smart_PLAT/LH2_dom,prints_PKD_1,pfscan_GPS_dom,pfscan_C-type_lectin,pfscan_PKD_dom,pfscan_PLAT/LH2_dom,pfscan_REJ-like,pfscan_WSC_carb-bd,tigrfam_Polycystin_cat	p.A1883in_frame_del	ENST00000262304.4	37	c.5650_5648	CCDS32369.1	16																																																																																				PKD1	-	superfamily_PKD_dom,smart_PKD/Chitinase_dom,pfscan_PKD_dom,tigrfam_Polycystin_cat		0.640	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PKD1	HGNC	protein_coding	OTTHUMT00000341688.1	0	0	0	63	63	16	0.00	0.00	CCG			2159520	-1	28	9	53	4	tier1	no_errors	ENST00000262304	ensembl	human	known	74_37	in_frame_del	34.57	69.23	DEL	1.000:1.000:1.000	-	28	53
POU3F1	5453	genome.wustl.edu	37	1	38511693	38511693	+	Silent	SNP	C	C	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr1:38511693C>T	ENST00000373012.2	-	1	757	c.723G>A	c.(721-723)gtG>gtA	p.V241V	RP5-884C9.2_ENST00000432922.1_lincRNA	NM_002699.3	NP_002690.3	Q03052	PO3F1_HUMAN	POU class 3 homeobox 1	241	Gly-rich.				axon ensheathment (GO:0008366)|forebrain development (GO:0030900)|keratinocyte differentiation (GO:0030216)|myelination in peripheral nervous system (GO:0022011)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|lung(1)|upper_aerodigestive_tract(1)	3	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AGTGCTCGCCCACCGATGAgc	0.731													ENSG00000185668																																					0													11.0	12.0	12.0					1																	38511693		2192	4284	6476	SO:0001819	synonymous_variant	0			-	L26494	CCDS30679.1	1p34.3	2011-06-20	2007-07-13		ENSG00000185668	ENSG00000185668		"""Homeoboxes / POU class"""	9214	protein-coding gene	gene with protein product		602479	"""POU domain class 3, transcription factor 1"""	OTF6		8451175	Standard	NM_002699		Approved	OCT6, SCIP	uc001ccp.1	Q03052	OTTHUMG00000000485	ENST00000373012.2:c.723G>A	1.37:g.38511693C>T			Q5TAG2	Silent	SNP	pfam_POU_specific,pfam_Homeobox_dom,superfamily_Lambda_D-bd_dom,superfamily_Homeodomain-like,smart_POU_specific,smart_Homeobox_dom,pirsf_Transcription_factor_POU,pfscan_Homeobox_dom,pfscan_POU_specific,prints_POU	p.V241	ENST00000373012.2	37	c.723	CCDS30679.1	1																																																																																			-	POU3F1	-	pirsf_Transcription_factor_POU		0.731	POU3F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POU3F1	HGNC	protein_coding	OTTHUMT00000001213.1	0	0	0	30	30	10	0.00	0.00	C	NM_002699		38511693	-1	14	5	15	7	tier1	no_errors	ENST00000373012	ensembl	human	known	74_37	silent	48.28	41.67	SNP	1.000	T	14	15
TIA1	7072	genome.wustl.edu	37	2	70441617	70441617	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr2:70441617delT	ENST00000433529.2	-	12	1108	c.898delA	c.(898-900)attfs	p.I300fs	TIA1_ENST00000482876.1_5'Flank|TIA1_ENST00000282574.4_Frame_Shift_Del_p.I299fs|TIA1_ENST00000415783.2_Frame_Shift_Del_p.I289fs|TIA1_ENST00000445587.1_Intron|C2orf42_ENST00000470096.1_Intron	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	300					apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						GGATATCCAATTTGATTCTGC	0.368													ENSG00000116001																																					0													55.0	50.0	52.0					2																	70441617		2203	4300	6503	SO:0001589	frameshift_variant	0					CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001		"""RNA binding motif (RRM) containing"""	11802	protein-coding gene	gene with protein product	"""T-cell-restricted intracellular antigen-1"", ""nucleolysin TIA-1 isoform p40"""	603518	"""TIA1 cytotoxic granule-associated RNA-binding protein"""			8176212, 12486009	Standard	NM_022173		Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000433529.2:c.898delA	2.37:g.70441617delT	ENSP00000401371:p.Ile300fs		Q53SS9	Frame_Shift_Del	DEL	pfam_RRM_dom,smart_RRM_dom_euk,smart_RRM_dom,pfscan_RRM_dom	p.I300fs	ENST00000433529.2	37	c.898	CCDS1901.1	2																																																																																				TIA1	-	NULL		0.368	TIA1-001	KNOWN	basic|CCDS	protein_coding	TIA1	HGNC	protein_coding	OTTHUMT00000251842.2	0	0	0	22	22	79	0.00	0.00	T	NM_022037		70441617	-1	38	34	10	7	tier1	no_errors	ENST00000433529	ensembl	human	known	74_37	frame_shift_del	79.17	82.93	DEL	1.000	-	38	10
ZDBF2	57683	genome.wustl.edu	37	2	207173373	207173373	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr2:207173373T>C	ENST00000374423.3	+	5	4507	c.4121T>C	c.(4120-4122)tTt>tCt	p.F1374S		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1374							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AATGACTCTTTTCAGGCAGCA	0.373													ENSG00000204186																																					0													47.0	45.0	46.0					2																	207173373		1832	4104	5936	SO:0001583	missense	0			-	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.4121T>C	2.37:g.207173373T>C	ENSP00000363545:p.Phe1374Ser		Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	pfam_Znf_DBF,smart_Znf_DBF	p.F1374S	ENST00000374423.3	37	c.4121	CCDS46501.1	2	.	.	.	.	.	.	.	.	.	.	T	10.53	1.376181	0.24857	.	.	ENSG00000204186	ENST00000374423	T	0.43688	0.94	3.63	1.2	0.21068	.	.	.	.	.	T	0.23649	0.0572	L	0.29908	0.895	0.09310	N	1	P	0.38978	0.652	B	0.30179	0.112	T	0.08764	-1.0706	9	0.22706	T	0.39	.	8.1435	0.31097	0.0:0.0:0.3314:0.6686	.	1374	Q9HCK1	ZDBF2_HUMAN	S	1374	ENSP00000363545:F1374S	ENSP00000363545:F1374S	F	+	2	0	ZDBF2	206881618	0.325000	0.24660	0.015000	0.15790	0.010000	0.07245	0.761000	0.26489	0.242000	0.21303	0.528000	0.53228	TTT	-	ZDBF2	-	NULL		0.373	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZDBF2	HGNC	protein_coding	OTTHUMT00000336458.1	0	0	0	27	27	118	0.00	0.00	T	NM_020923		207173373	+1	50	88	2	9	tier1	no_errors	ENST00000374423	ensembl	human	known	74_37	missense	96.15	90.72	SNP	0.022	C	50	2
ZNF595	152687	genome.wustl.edu	37	4	86907	86907	+	3'UTR	SNP	G	G	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr4:86907G>T	ENST00000339368.6	+	0	1716							Q8IYB9	ZN595_HUMAN	zinc finger protein 595						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TCATACTGGAGAGAAACCCTA	0.373													ENSG00000197701																																					0													46.0	52.0	50.0					4																	86907		2109	4253	6362	SO:0001624	3_prime_UTR_variant	0			-	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000339368.6:c.*1713G>T	4.37:g.86907G>T				R	SNP	-	NULL	ENST00000339368.6	37	NULL		4																																																																																			-	ZNF595	-	-		0.373	ZNF595-001	KNOWN	basic	processed_transcript	ZNF595	HGNC	protein_coding	OTTHUMT00000357814.2	0	0	0	16	16	20	0.00	0.00	G	NM_182524		86907	+1	23	14	3	2	tier1	no_errors	ENST00000339368	ensembl	human	known	74_37	rna	88.46	82.35	SNP	1.000	T	23	3
EYS	346007	genome.wustl.edu	37	6	66045003	66045003	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr6:66045003C>G	ENST00000370621.3	-	11	2162	c.1636G>C	c.(1636-1638)Gac>Cac	p.D546H	EYS_ENST00000370616.2_Missense_Mutation_p.D546H|EYS_ENST00000370618.3_Missense_Mutation_p.D546H|EYS_ENST00000342421.5_Missense_Mutation_p.D546H|EYS_ENST00000503581.1_Missense_Mutation_p.D546H|EYS_ENST00000393380.2_Missense_Mutation_p.D546H			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	546					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCCTGACTGTCTTCTTCACTC	0.353													ENSG00000188107																																					0													154.0	142.0	146.0					6																	66045003		2203	4300	6503	SO:0001583	missense	0			-		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1636G>C	6.37:g.66045003C>G	ENSP00000359655:p.Asp546His		A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	pfam_Laminin_G,pfam_EG-like_dom,superfamily_ConA-like_lec_gl_sf,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,smart_Laminin_G,pfscan_EG-like_dom,pfscan_Laminin_G	p.D546H	ENST00000370621.3	37	c.1636		6	.	.	.	.	.	.	.	.	.	.	c	9.312	1.055739	0.19907	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83	3.8	2.85	0.33270	.	.	.	.	.	T	0.06690	0.0171	L	0.32530	0.975	0.09310	N	1	B;P;B	0.35242	0.16;0.492;0.36	B;B;B	0.30855	0.04;0.121;0.099	T	0.18053	-1.0349	9	0.21014	T	0.42	.	9.7053	0.40211	0.0:0.7874:0.2126:0.0	.	546;546;546	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	H	546	ENSP00000424243:D546H;ENSP00000359655:D546H;ENSP00000359650:D546H;ENSP00000377042:D546H;ENSP00000341818:D546H;ENSP00000359652:D546H	ENSP00000341818:D546H	D	-	1	0	EYS	66101724	0.901000	0.30685	0.228000	0.23943	0.028000	0.11728	0.396000	0.20867	1.834000	0.53371	0.491000	0.48974	GAC	-	EYS	-	NULL		0.353	EYS-001	KNOWN	basic	protein_coding	EYS	HGNC	protein_coding	OTTHUMT00000351351.3	0	0	0	12	12	62	0.00	0.00	C	XM_294050		66045003	-1	10	4	25	60	tier1	no_errors	ENST00000370616	ensembl	human	known	74_37	missense	28.57	6.25	SNP	0.249	G	10	25
PKHD1L1	93035	genome.wustl.edu	37	8	110456116	110456116	+	Silent	SNP	C	C	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr8:110456116C>T	ENST00000378402.5	+	37	4880	c.4776C>T	c.(4774-4776)ctC>ctT	p.L1592L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1592	IPT/TIG 8.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTAGTAATCTCCCATGGGCTA	0.308										HNSCC(38;0.096)			ENSG00000205038																																					0													92.0	88.0	90.0					8																	110456116		1818	4073	5891	SO:0001819	synonymous_variant	0			-	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.4776C>T	8.37:g.110456116C>T			Q567P2|Q9UF27	Silent	SNP	pfam_IPT,pfam_G8_domain,pfam_PA14,superfamily_Ig_E-set,superfamily_Pectin_lyase_fold/virulence,superfamily_Cupredoxin,smart_IPT,smart_PA14,smart_PbH1	p.L1592	ENST00000378402.5	37	c.4776	CCDS47911.1	8																																																																																			-	PKHD1L1	-	pfam_IPT,superfamily_Ig_E-set,smart_IPT		0.308	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKHD1L1	HGNC	protein_coding	OTTHUMT00000381017.1	0	0	2	39	39	135	0.00	1.46	C	NM_177531		110456116	+1	25	55	21	60	tier1	no_errors	ENST00000378402	ensembl	human	known	74_37	silent	54.35	47.83	SNP	0.689	T	25	21
AUTS2	26053	genome.wustl.edu	37	7	70254924	70254924	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr7:70254924G>T	ENST00000342771.4	+	19	3043	c.2722G>T	c.(2722-2724)Gag>Tag	p.E908*	AUTS2_ENST00000406775.2_Nonsense_Mutation_p.E884*	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	908										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GGCCGCCGACGAGCACAAGGC	0.672													ENSG00000158321																																					0													31.0	31.0	31.0					7																	70254924		2200	4300	6500	SO:0001587	stop_gained	0			-	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2722G>T	7.37:g.70254924G>T	ENSP00000344087:p.Glu908*		A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Nonsense_Mutation	SNP	prints_AUTS2	p.E908*	ENST00000342771.4	37	c.2722	CCDS5539.1	7	.	.	.	.	.	.	.	.	.	.	G	42	9.270267	0.99120	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	.	.	.	4.28	4.28	0.50868	.	0.201130	0.51477	D	0.000088	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.6153	16.9403	0.86216	0.0:0.0:1.0:0.0	.	.	.	.	X	884;908	.	.	E	+	1	0	AUTS2	69892860	1.000000	0.71417	0.934000	0.37439	0.951000	0.60555	9.314000	0.96306	2.223000	0.72356	0.655000	0.94253	GAG	-	AUTS2	-	NULL		0.672	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AUTS2	HGNC	protein_coding	OTTHUMT00000251971.2	0	0	0	20	20	10	0.00	0.00	G			70254924	+1	5	0	23	7	tier1	no_errors	ENST00000342771	ensembl	human	known	74_37	nonsense	17.86	0.00	SNP	0.999	T	5	23
OTOG	340990	genome.wustl.edu	37	11	17663399	17663399	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr11:17663399G>T	ENST00000399391.2	+	51	8232	c.8232G>T	c.(8230-8232)caG>caT	p.Q2744H	OTOG_ENST00000399397.1_Missense_Mutation_p.Q2671H	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	2744					adult locomotory behavior (GO:0008344)|L-arabinose metabolic process (GO:0046373)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	alpha-L-arabinofuranosidase activity (GO:0046556)|structural molecule activity (GO:0005198)			breast(3)|central_nervous_system(1)|lung(1)|skin(1)	6						TGTAGAACCAGGAGTACGAGC	0.647													ENSG00000188162																																					0																																										SO:0001583	missense	0			-	AK128214	CCDS59225.1	11p14.3	2014-07-17			ENSG00000188162	ENSG00000188162			8516	protein-coding gene	gene with protein product		604487				9405633	Standard	NM_001277269		Approved	mlemp, OTGN, FLJ46346	uc031pzc.1	Q6ZRI0	OTTHUMG00000149905	ENST00000399391.2:c.8232G>T	11.37:g.17663399G>T	ENSP00000382323:p.Gln2744His		A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_AbfB,pfam_TIL_dom,superfamily_AbfB,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_EG-like_dom	p.Q2744H	ENST00000399391.2	37	c.8232	CCDS59225.1	11	.	.	.	.	.	.	.	.	.	.	G	13.17	2.155775	0.38021	.	.	ENSG00000188162	ENST00000399391;ENST00000399397	T;T	0.18016	2.24;2.35	5.09	2.16	0.27623	.	0.000000	0.53938	U	0.000050	T	0.23370	0.0565	M	0.73962	2.25	0.44789	D	0.997791	.	.	.	.	.	.	T	0.04579	-1.0941	8	0.14656	T	0.56	.	6.4623	0.21964	0.3354:0.0:0.6646:0.0	.	.	.	.	H	2744;2671	ENSP00000382323:Q2744H;ENSP00000382329:Q2671H	ENSP00000382323:Q2744H	Q	+	3	2	OTOG	17619975	1.000000	0.71417	1.000000	0.80357	0.125000	0.20455	1.261000	0.32980	1.157000	0.42530	-0.671000	0.03813	CAG	-	OTOG	-	NULL		0.647	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	OTOG	HGNC	protein_coding		0	0	0	40	40	15	0.00	0.00	G			17663399	+1	4	0	26	6	tier1	no_errors	ENST00000399391	ensembl	human	known	74_37	missense	13.33	0.00	SNP	1.000	T	4	26
CABLES1	91768	genome.wustl.edu	37	18	20716015	20716023	+	In_Frame_Del	DEL	GGCGCCGGC	GGCGCCGGC	-	rs201595073|rs139352344	byFrequency	TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	GGCGCCGGC	GGCGCCGGC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr18:20716015_20716023delGGCGCCGGC	ENST00000256925.7	+	1	289_297	c.289_297delGGCGCCGGC	c.(289-297)ggcgccggcdel	p.GAG97del	AC105247.1_ENST00000411067.1_RNA|CABLES1_ENST00000400473.2_Intron	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	97	Ala-rich.|Interacts with TDRD7. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ggccaagccgggcgccggcggcgcctgcg	0.785													ENSG00000134508		1123	0.224241	0.2602	0.17	5008	,	,		3844	0.244		0.2048	False		,,,				2504	0.2137																0																																										SO:0001651	inframe_deletion	0				BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.289_297delGGCGCCGGC	18.37:g.20716015_20716023delGGCGCCGGC	ENSP00000256925:p.Gly97_Gly99del		B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	In_Frame_Del	DEL	pfam_Cyclin_N,superfamily_Cyclin-like,pirsf_Cdk5/c-Abl_linker_Cables	p.GGA99in_frame_del	ENST00000256925.7	37	c.289_297	CCDS42417.1	18																																																																																				CABLES1	-	pirsf_Cdk5/c-Abl_linker_Cables		0.785	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CABLES1	HGNC	protein_coding	OTTHUMT00000445198.2	0	0	0	0	0	0	0.00	0.00	GGCGCCGGC	NM_138375		20716023	+1	0	0	1	1	tier1	no_errors	ENST00000256925	ensembl	human	known	74_37	in_frame_del	0.00	0.00	DEL	0.983:0.981:0.990:0.998:0.999:0.997:0.999:0.999:0.997	-	0	1
FAM115C	285966	genome.wustl.edu	37	7	143417912	143417912	+	Intron	SNP	C	C	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr7:143417912C>T	ENST00000441159.2	+	3	1681				FAM115C_ENST00000425618.2_Intron|FAM115C_ENST00000411497.2_Intron|FAM115C_ENST00000409703.3_Silent_p.V379V|FAM115C_ENST00000411935.1_Silent_p.V379V|FAM115C_ENST00000357344.4_Intron|FAM115C_ENST00000444908.2_Intron			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C						hematopoietic progenitor cell differentiation (GO:0002244)					endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						ctcactctgtcatccaggttg	0.488													ENSG00000170379																																					0																																										SO:0001627	intron_variant	0			-	AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"""family with sequence similarity 139, member A"""	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.1615+145C>T	7.37:g.143417912C>T			B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Silent	SNP	NULL	p.V379	ENST00000441159.2	37	c.1137		7																																																																																			-	FAM115C	-	NULL		0.488	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	FAM115C	HGNC	protein_coding	OTTHUMT00000330287.1	0	0	0	59	59	0	0.00	0.00	C	NM_173678		143417912	+1	119	0	22	0	tier1	no_errors	ENST00000409703	ensembl	human	known	74_37	silent	84.40	0.00	SNP	0.092	T	119	22
MUC4	4585	genome.wustl.edu	37	3	195513948	195513948	+	Silent	SNP	G	G	A			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr3:195513948G>A	ENST00000463781.3	-	2	4962	c.4503C>T	c.(4501-4503)caC>caT	p.H1501H	MUC4_ENST00000475231.1_Silent_p.H1501H|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAGTGACGTGACCTGTGG	0.567													ENSG00000145113																																					0													2.0	2.0	2.0					3																	195513948		387	998	1385	SO:0001819	synonymous_variant	0			-	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4503C>T	3.37:g.195513948G>A			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EG-like_dom,pfscan_AMOP,pfscan_EG-like_dom	p.H1501	ENST00000463781.3	37	c.4503	CCDS54700.1	3																																																																																			-	MUC4	-	NULL		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	0	0	0	42	42	0	0.00	0.00	G	NM_018406		195513948	-1	18	0	29	0	tier1	no_errors	ENST00000463781	ensembl	human	known	74_37	silent	38.30	0.00	SNP	0.000	A	18	29
NRXN1	9378	genome.wustl.edu	37	2	50147836	50147847	+	3'UTR	DEL	GTGTGTGTGTGT	GTGTGTGTGTGT	-	rs200264093|rs201814381|rs199597709|rs199689866|rs368179294|rs200666696|rs200969250|rs66612444		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	GTGTGTGTGTGT	GTGTGTGTGTGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr2:50147836_50147847delGTGTGTGTGTGT	ENST00000406316.2	-	0	7145_7156				NRXN1_ENST00000401710.1_3'UTR|NRXN1_ENST00000404971.1_3'UTR|NRXN1_ENST00000342183.5_3'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						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)			CTGTGGATTCgtgtgtgtgtgtgtgtgtgtgt	0.392													ENSG00000179915																																					0																																										SO:0001624	3_prime_UTR_variant	0				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.*1246ACACACACACAC>-	2.37:g.50147836_50147847delGTGTGTGTGTGT			A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	R	DEL	-	NULL	ENST00000406316.2	37	NULL	CCDS54360.1	2																																																																																				NRXN1	-	-		0.392	NRXN1-001	KNOWN	basic|CCDS	protein_coding	NRXN1	HGNC	protein_coding	OTTHUMT00000325291.2	0	0	0	0	0	0	0.00	0.00	GTGTGTGTGTGT			50147847	-1	0	0	0	0	tier1	no_errors	ENST00000484192	ensembl	human	known	74_37	rna	0.00	0.00	DEL	0.000:0.001:0.005:0.106:0.113:0.127:0.107:0.109:0.093:0.096:0.025:0.055	-	0	0
GRHPR	9380	genome.wustl.edu	37	9	37430971	37430971	+	Intron	SNP	G	G	T			TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr9:37430971G>T	ENST00000318158.6	+	7	819				GRHPR_ENST00000607784.1_Intron	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase						cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		CTGGACTTGAGGATCTGAAGG	0.622													ENSG00000137106																																					0																																										SO:0001627	intron_variant	0			-	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.734+328G>T	9.37:g.37430971G>T			Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	pfam_D-isomer_2_OHA_DH_D-bd	p.E211D	ENST00000318158.6	37	c.633	CCDS6609.1	9	.	.	.	.	.	.	.	.	.	.	G	7.165	0.586469	0.13749	.	.	ENSG00000137106	ENST00000377824;ENST00000438860	D	0.83591	-1.74	2.72	-5.44	0.02624	.	.	.	.	.	T	0.69006	0.3063	.	.	.	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.51244	-0.8730	8	0.87932	D	0	.	3.1136	0.06367	0.1148:0.458:0.2474:0.1798	.	354;211	Q5T946;Q9H636	.;.	D	354;211	ENSP00000367055:E354D	ENSP00000367055:E354D	E	+	3	2	GRHPR	37420971	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.863000	0.00725	-2.422000	0.00563	-1.193000	0.01689	GAG	-	GRHPR	-	NULL		0.622	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GRHPR	HGNC	protein_coding	OTTHUMT00000052442.1	0	0	0	28	28	86	0.00	0.00	G	NM_012203		37430971	+1	4	2	46	67	tier1	no_errors	ENST00000494290	ensembl	human	known	74_37	missense	8.00	2.90	SNP	0.000	T	4	46
LINC01287	103724390	genome.wustl.edu	37	7	153110008	153110008	+	lincRNA	SNP	A	A	G	rs112770540		TCGA-DX-A48L-01A-11D-A307-09	TCGA-DX-A48L-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	f55dccaa-44da-4482-93a8-7853325f5bea	b83395ce-e95f-4de3-a722-0e785b4e2887	g.chr7:153110008A>G	ENST00000416982.1	-	0	1040																											agatggcggcagtgcagaagg	0.537													ENSG00000234722																																					0													69.0	78.0	75.0					7																	153110008		692	1591	2283			0			-																													7.37:g.153110008A>G				R	SNP	-	NULL	ENST00000416982.1	37	NULL		7																																																																																			rs112770540	AC073236.3	-	-		0.537	AC073236.3-001	KNOWN	basic	lincRNA	ENSG00000234722	Clone_based_vega_gene	lincRNA	OTTHUMT00000280517.1	0	0	0	41	41	26	0.00	0.00	A			153110008	-1	8	2	90	35	tier1	no_errors	ENST00000416982	ensembl	human	known	74_37	rna	8.16	5.41	SNP	0.157	G	8	90
