#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CRELD2	79174	broad.mit.edu	37	22	50316920	50316920	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr22:50316920G>A	ENST00000328268.4	+	7	801	c.727G>A	c.(727-729)Gct>Act	p.A243T	CRELD2_ENST00000404488.3_Missense_Mutation_p.A292T|CRELD2_ENST00000407217.3_Missense_Mutation_p.A243T|CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000403427.3_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	243						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TCCCTGCAGCGCTGCGCAGTT	0.692																																						ENST00000404488.3																			0				endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9						c.(874-876)Gct>Act		cysteine-rich with EGF-like domains 2							21.0	24.0	23.0					22																	50316920		2201	4295	6496	SO:0001583	missense	79174					endoplasmic reticulum|extracellular region	calcium ion binding	g.chr22:50316920G>A	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.727G>A	22.37:g.50316920G>A	ENSP00000332223:p.Ala243Thr					CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000407217.3_Missense_Mutation_p.A243T|CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000328268.4_Missense_Mutation_p.A243T	p.A292T	NM_001135101.1	NP_001128573.1	Q6UXH1	CREL2_HUMAN		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)	8	1009	+		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)	243			EGF-like 2; calcium-binding (Potential).		A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	c.874G>A	CCDS14082.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629362	0.28978	.	.	ENSG00000184164	ENST00000404488;ENST00000328268;ENST00000407217	T;T;D	0.92397	0.62;0.42;-3.03	4.57	-0.118	0.13547	EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);	0.757438	0.12278	N	0.483217	T	0.76190	0.3953	N	0.16656	0.425	0.09310	N	0.999999	B;B;P;B;B	0.39094	0.09;0.371;0.659;0.111;0.072	B;B;B;B;B	0.21708	0.005;0.031;0.036;0.004;0.004	T	0.67941	-0.5540	10	0.13470	T	0.59	.	4.5619	0.12165	0.3352:0.0:0.5199:0.145	.	243;292;243;243;243	Q6UXH1-2;Q6UXH1-5;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;CREL2_HUMAN;.	T	292;243;243	ENSP00000383938:A292T;ENSP00000332223:A243T;ENSP00000386034:A243T	ENSP00000332223:A243T	A	+	1	0	CRELD2	48702924	0.822000	0.29219	0.000000	0.03702	0.000000	0.00434	3.180000	0.50895	-0.215000	0.10063	-0.482000	0.04802	GCT		0.692	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		14	26	0	0	0	1	0	14	26				
PRKD2	25865	broad.mit.edu	37	19	47197153	47197153	+	Missense_Mutation	SNP	C	C	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr19:47197153C>A	ENST00000291281.4	-	10	1780	c.1555G>T	c.(1555-1557)Gcc>Tcc	p.A519S	PRKD2_ENST00000433867.1_Missense_Mutation_p.A519S|PRKD2_ENST00000595515.1_Missense_Mutation_p.A519S|PRKD2_ENST00000600194.1_Missense_Mutation_p.A362S|PRKD2_ENST00000601806.1_Missense_Mutation_p.A362S			Q9BZL6	KPCD2_HUMAN	protein kinase D2	519					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		TGGCCTGGGGCGCTGGGTGCG	0.672																																						ENST00000433867.1																			0				central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41						c.(1555-1557)Gcc>Tcc		protein kinase D2							54.0	58.0	57.0					19																	47197153		2203	4300	6503	SO:0001583	missense	25865				cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity	g.chr19:47197153C>A	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.1555G>T	19.37:g.47197153C>A	ENSP00000291281:p.Ala519Ser					PRKD2_ENST00000595515.1_Missense_Mutation_p.A519S|PRKD2_ENST00000600194.1_Missense_Mutation_p.A362S|PRKD2_ENST00000291281.4_Missense_Mutation_p.A519S|PRKD2_ENST00000601806.1_Missense_Mutation_p.A362S	p.A519S	NM_001079880.1|NM_001079881.1|NM_016457.4	NP_001073349.1|NP_001073350.1|NP_057541.2	Q9BZL6	KPCD2_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)	11	2032	-		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)	519					Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	37	c.1555G>T	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	5.637	0.302135	0.10678	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.64991	-0.13;-0.13	5.08	-2.62	0.06152	.	0.150448	0.42548	D	0.000695	T	0.31918	0.0812	N	0.08118	0	0.29016	N	0.886558	B;B	0.15473	0.001;0.013	B;B	0.17979	0.008;0.02	T	0.35549	-0.9784	10	0.07175	T	0.84	-14.5096	11.0448	0.47852	0.0:0.4617:0.0:0.5383	.	519;519	E7ER94;Q9BZL6	.;KPCD2_HUMAN	S	519	ENSP00000291281:A519S;ENSP00000393978:A519S	ENSP00000291281:A519S	A	-	1	0	PRKD2	51888993	0.004000	0.15560	0.472000	0.27241	0.953000	0.61014	0.112000	0.15479	-0.234000	0.09782	0.555000	0.69702	GCC		0.672	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		13	44	1	0	7.93312e-07	1	8.96788e-07	13	44				
TTI1	9675	broad.mit.edu	37	20	36640810	36640810	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr20:36640810C>T	ENST00000373448.2	-	3	1647	c.1409G>A	c.(1408-1410)cGc>cAc	p.R470H	TTI1_ENST00000487362.1_5'UTR|TTI1_ENST00000373447.3_Missense_Mutation_p.R470H|TTI1_ENST00000449821.1_Missense_Mutation_p.R470H	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	470					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						CCTCTGGATGCGGTTCCAAGG	0.463																																						ENST00000373448.2																			0				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						c.(1408-1410)cGc>cAc		TELO2 interacting protein 1							63.0	67.0	66.0					20																	36640810		2203	4300	6503	SO:0001583	missense	9675						binding	g.chr20:36640810C>T	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.1409G>A	20.37:g.36640810C>T	ENSP00000362547:p.Arg470His					TTI1_ENST00000487362.1_5'UTR|TTI1_ENST00000373447.3_Missense_Mutation_p.R470H|TTI1_ENST00000449821.1_Missense_Mutation_p.R470H	p.R470H	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN			3	1647	-			470					D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	c.1409G>A	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	c	0.557	-0.847090	0.02651	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.68479	-0.33;-0.33;-0.33	5.08	-1.07	0.09968	Armadillo-type fold (1);	1.096590	0.06874	N	0.801308	T	0.50718	0.1632	N	0.25647	0.755	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.34378	-0.9831	10	0.40728	T	0.16	-25.4045	7.537	0.27717	0.0:0.5185:0.1562:0.3253	.	470	O43156	TTI1_HUMAN	H	470	ENSP00000362547:R470H;ENSP00000362546:R470H;ENSP00000407270:R470H	ENSP00000362546:R470H	R	-	2	0	TTI1	36074224	0.001000	0.12720	0.000000	0.03702	0.286000	0.27126	0.351000	0.20096	-0.395000	0.07715	-0.285000	0.09966	CGC		0.463	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		3	63	0	0	0	1	0	3	63				
SORCS3	22986	broad.mit.edu	37	10	106982994	106982994	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr10:106982994G>A	ENST00000369701.3	+	20	3082	c.2855G>A	c.(2854-2856)gGc>gAc	p.G952D	SORCS3_ENST00000369699.4_3'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	952					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGGTGGTTCGGCAATAGCACA	0.458																																					NSCLC(116;1497 1690 7108 13108 14106)	ENST00000369701.3																			0				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131						c.(2854-2856)gGc>gAc		sortilin-related VPS10 domain containing receptor 3							200.0	193.0	196.0					10																	106982994		2203	4300	6503	SO:0001583	missense	22986					integral to membrane	neuropeptide receptor activity	g.chr10:106982994G>A	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2855G>A	10.37:g.106982994G>A	ENSP00000358715:p.Gly952Asp					SORCS3_ENST00000369699.4_3'UTR	p.G952D	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)	20	3082	+		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)	952					Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	c.2855G>A	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032574	0.54790	.	.	ENSG00000156395	ENST00000369701	T	0.59906	0.23	5.06	5.06	0.68205	PKD domain (1);	0.329234	0.33040	N	0.005351	T	0.59838	0.2223	M	0.69523	2.12	0.80722	D	1	B	0.27166	0.17	B	0.28465	0.09	T	0.57911	-0.7729	9	.	.	.	.	18.7786	0.91922	0.0:0.0:1.0:0.0	.	952	Q9UPU3	SORC3_HUMAN	D	952	ENSP00000358715:G952D	.	G	+	2	0	SORCS3	106972984	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.087000	0.64480	2.516000	0.84829	0.563000	0.77884	GGC		0.458	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		5	196	0	0	0	1	0	5	196				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																197331							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	140	0	0	0	1	0	4	140				
NRSN2	80023	broad.mit.edu	37	20	333947	333947	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr20:333947G>A	ENST00000382291.3	+	4	523	c.283G>A	c.(283-285)Gag>Aag	p.E95K	NRSN2_ENST00000382285.2_Missense_Mutation_p.E95K|NRSN2_ENST00000492242.1_3'UTR|NRSN2_ENST00000608736.1_Intron	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN	neurensin 2	95						integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8		all_cancers(10;0.0834)				GGGCATCGGTGAGGGTGAGTT	0.652																																						ENST00000382291.3																			0				endometrium(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8						c.(283-285)Gag>Aag		neurensin 2							87.0	82.0	84.0					20																	333947		2203	4300	6503	SO:0001583	missense	80023					integral to membrane|plasma membrane|transport vesicle		g.chr20:333947G>A	AL136915	CCDS12996.1	20p13	2008-02-04	2006-07-04	2006-07-04	ENSG00000125841	ENSG00000125841			16229	protein-coding gene	gene with protein product		610666	"""chromosome 20 open reading frame 98"""	C20orf98		16527258	Standard	NM_024958		Approved	dJ1103G7.6	uc002wdi.4	Q9GZP1	OTTHUMG00000031628	ENST00000382291.3:c.283G>A	20.37:g.333947G>A	ENSP00000371728:p.Glu95Lys					NRSN2_ENST00000382285.2_Missense_Mutation_p.E95K|NRSN2_ENST00000492242.1_3'UTR	p.E95K	NM_024958.2	NP_079234.1	Q9GZP1	NRSN2_HUMAN			4	523	+		all_cancers(10;0.0834)	95					A8K3B2|Q6FII5|Q9NUD3	Missense_Mutation	SNP	ENST00000382291.3	37	c.283G>A	CCDS12996.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.348610	0.41599	.	.	ENSG00000125841	ENST00000382291;ENST00000382285	T;T	0.18960	2.18;2.18	4.76	2.76	0.32466	.	0.421310	0.24511	N	0.037885	T	0.17662	0.0424	L	0.56769	1.78	0.09310	N	1	B	0.29037	0.231	B	0.25291	0.059	T	0.16660	-1.0395	10	0.42905	T	0.14	-4.051	5.2707	0.15622	0.1043:0.0:0.6729:0.2228	.	95	Q9GZP1	NRSN2_HUMAN	K	95	ENSP00000371728:E95K;ENSP00000371722:E95K	ENSP00000371722:E95K	E	+	1	0	NRSN2	281947	0.279000	0.24239	0.001000	0.08648	0.979000	0.70002	2.845000	0.48254	0.570000	0.29347	0.643000	0.83706	GAG		0.652	NRSN2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077446.1	NM_024958		4	78	0	0	0	1	0	4	78				
SNHG14	104472715	broad.mit.edu	37	15	25467500	25467500	+	RNA	SNP	G	G	C			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr15:25467500G>C	ENST00000424208.1	+	0	6332				SNORD115-28_ENST00000363931.1_RNA|SNORD115-30_ENST00000364117.1_RNA|SNHG14_ENST00000453082.2_RNA|SNORD115-27_ENST00000364430.1_RNA|SNORD115-29_ENST00000362834.1_RNA	NR_003305.1				small nucleolar RNA host gene 14 (non-protein coding)																		GGTTGGGGTGGTGATGAGAAC	0.522																																						ENST00000453082.2																			0																																																			104472715							g.chr15:25467500G>C			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25467500G>C						SNORD115-28_ENST00000363931.1_RNA		NR_003343.1						0	753	+									RNA	SNP	ENST00000424208.1	37																																																																																						0.522	SNHG14-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000126729.2			84	195	0	0	0	1	0	84	195				
FOXD4	2298	broad.mit.edu	37	9	117692	117692	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr9:117692C>T	ENST00000382500.2	-	1	725	c.428G>A	c.(427-429)cGc>cAc	p.R143H		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	143					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GGGGAACTTGCGGCGGTAGTA	0.642																																						ENST00000382500.2																			0				endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14						c.(427-429)cGc>cAc		forkhead box D4							41.0	67.0	58.0					9																	117692		2098	4152	6250	SO:0001583	missense	2298				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr9:117692C>T	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.428G>A	9.37:g.117692C>T	ENSP00000371940:p.Arg143His						p.R143H	NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)	1	725	-	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	143					B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	c.428G>A	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	16.90	3.250380	0.59212	.	.	ENSG00000170122	ENST00000382500	D	0.95518	-3.73	2.24	2.24	0.28232	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.35870	U	0.002935	D	0.91099	0.7198	N	0.03194	-0.395	0.32415	N	0.550161	D	0.76494	0.999	D	0.67725	0.953	D	0.88700	0.3215	10	0.72032	D	0.01	.	3.6941	0.08357	0.0:0.5791:0.2634:0.1575	.	143	Q12950	FOXD4_HUMAN	H	143	ENSP00000371940:R143H	ENSP00000371940:R143H	R	-	2	0	FOXD4	107692	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.898000	0.48672	1.253000	0.44018	0.291000	0.19559	CGC		0.642	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305		6	371	0	0	0	1	0	6	371				
SUN1	23353	broad.mit.edu	37	7	882981	882981	+	Missense_Mutation	SNP	G	G	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr7:882981G>T	ENST00000405266.1	+	5	506	c.482G>T	c.(481-483)gGa>gTa	p.G161V	SUN1_ENST00000452783.2_Intron|SUN1_ENST00000457378.2_Missense_Mutation_p.G182V|SUN1_ENST00000425407.2_Missense_Mutation_p.G111V|SUN1_ENST00000401592.1_Missense_Mutation_p.G161V|SUN1_ENST00000403868.1_Missense_Mutation_p.G161V|SUN1_ENST00000389574.3_Missense_Mutation_p.G111V|SUN1_ENST00000456758.2_Missense_Mutation_p.G219V			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	161					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ACTTTAGGTGGAAATAAAGCT	0.468																																						ENST00000456758.2																			0				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(655-657)gGa>gTa		Sad1 and UNC84 domain containing 1							74.0	83.0	80.0					7																	882981		1932	4113	6045	SO:0001583	missense	23353				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding	g.chr7:882981G>T	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.482G>T	7.37:g.882981G>T	ENSP00000384116:p.Gly161Val					SUN1_ENST00000457378.2_Missense_Mutation_p.G182V|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000401592.1_Missense_Mutation_p.G161V|SUN1_ENST00000425407.2_Missense_Mutation_p.G111V|SUN1_ENST00000389574.3_Missense_Mutation_p.G111V|SUN1_ENST00000405266.1_Missense_Mutation_p.G161V|SUN1_ENST00000403868.1_Missense_Mutation_p.G161V	p.G219V			O94901	SUN1_HUMAN			8	656	+			161			SYNE2-binding.		A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37	c.656G>T		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.62|11.62	1.691605|1.691605	0.30052|0.30052	.|.	.|.	ENSG00000164828|ENSG00000164828	ENST00000419312|ENST00000456758;ENST00000389574;ENST00000457378;ENST00000435699;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407	.|T;T;T;T;T;T;T;T	.|0.54479	.|2.13;1.56;0.79;0.57;2.14;2.13;0.81;1.56	4.59|4.59	2.66|2.66	0.31614|0.31614	.|.	.|0.648698	.|0.15865	.|N	.|0.240810	.|T	.|0.59878	.|0.2226	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	.|P;D;P;P	.|0.61697	.|0.825;0.99;0.886;0.484	.|P;P;P;B	.|0.52909	.|0.511;0.713;0.586;0.207	.|T	.|0.55736	.|-0.8094	.|10	.|0.33141	.|T	.|0.24	-10.4919|-10.4919	10.5913|10.5913	0.45310|0.45310	0.0:0.1448:0.7049:0.1503|0.0:0.1448:0.7049:0.1503	.|.	.|161;182;111;161	.|E9PF23;F8WD13;O94901-5;O94901-3	.|.;.;.;.	X|V	2|219;111;182;161;161;161;161;161;111	.|ENSP00000388743:G219V;ENSP00000374225:G111V;ENSP00000395952:G182V;ENSP00000388430:G161V;ENSP00000384116:G161V;ENSP00000384015:G161V;ENSP00000383947:G161V;ENSP00000392309:G111V	.|ENSP00000297445:G161V	E|G	+|+	1|2	0|0	SUN1|SUN1	849507|849507	1.000000|1.000000	0.71417|0.71417	0.638000|0.638000	0.29380|0.29380	0.705000|0.705000	0.40729|0.40729	3.411000|3.411000	0.52672|0.52672	0.421000|0.421000	0.25980|0.25980	0.591000|0.591000	0.81541|0.81541	GAA|GGA		0.468	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		11	133	1	0	3.07112e-06	1	3.32704e-06	11	133				
WDR63	126820	broad.mit.edu	37	1	85547042	85547042	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr1:85547042G>A	ENST00000294664.6	+	4	409	c.229G>A	c.(229-231)Gac>Aac	p.D77N	WDR63_ENST00000326813.8_Missense_Mutation_p.D77N|WDR63_ENST00000370596.1_Missense_Mutation_p.D77N	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	77										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		CATTTTTGAGGACCTGCGCAA	0.378																																						ENST00000294664.6																			0				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36						c.(229-231)Gac>Aac		WD repeat domain 63							107.0	108.0	108.0					1																	85547042		2203	4300	6503	SO:0001583	missense	126820							g.chr1:85547042G>A		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.229G>A	1.37:g.85547042G>A	ENSP00000294664:p.Asp77Asn					WDR63_ENST00000370596.1_Missense_Mutation_p.D77N|WDR63_ENST00000326813.8_Missense_Mutation_p.D77N	p.D77N	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN		all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)	4	409	+			77					A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	c.229G>A	CCDS702.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854088	0.71719	.	.	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664;ENST00000528899	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.61702	0.2368	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.54370	-0.8304	10	0.35671	T	0.21	-0.447	20.1484	0.98083	0.0:0.0:1.0:0.0	.	77;77	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	N	77;77;77;64	ENSP00000359628:D77N;ENSP00000317463:D77N;ENSP00000294664:D77N;ENSP00000435102:D64N	ENSP00000294664:D77N	D	+	1	0	WDR63	85319630	1.000000	0.71417	0.197000	0.23402	0.045000	0.14185	9.135000	0.94478	2.770000	0.95276	0.650000	0.86243	GAC		0.378	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		21	34	0	0	0	1	0	21	34				
MLLT3	4300	broad.mit.edu	37	9	20414346	20414346	+	Silent	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr9:20414346G>A	ENST00000380338.4	-	5	784	c.498C>T	c.(496-498)agC>agT	p.S166S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	166	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S166S(4)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctactgctgctgctgc	0.527			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		4	Substitution - coding silent(4)	p.S166S(4)	urinary_tract(2)|lung(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(496-498)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414346		1434	3114	4548	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414346G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.498C>T	9.37:g.20414346G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S	p.S166S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	784	-			166			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.498C>T	CCDS6494.1																																																																																				0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		4	70	0	0	0	1	0	4	70				
MGAM	8972	broad.mit.edu	37	7	141708443	141708443	+	Nonsense_Mutation	SNP	G	G	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr7:141708443G>T	ENST00000549489.2	+	3	360	c.265G>T	c.(265-267)Gaa>Taa	p.E89*	MGAM_ENST00000475668.2_Nonsense_Mutation_p.E89*	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	89	P-type 1. {ECO:0000255|PROSITE- ProRule:PRU00779}.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGTTTCTGCTGAATGTCCAGT	0.448																																						ENST00000475668.2																			0				cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13						c.(265-267)Gaa>Taa		maltase-glucoamylase (alpha-glucosidase)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)						94.0	92.0	93.0					7																	141708443		1887	4105	5992	SO:0001587	stop_gained	8972				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity	g.chr7:141708443G>T	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.265G>T	7.37:g.141708443G>T	ENSP00000447378:p.Glu89*					MGAM_ENST00000549489.2_Nonsense_Mutation_p.E89*	p.E89*			O43451	MGA_HUMAN			3	319	+	Melanoma(164;0.0272)		89			P-type 1.		Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000549489.2	37	c.265G>T	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.010148	0.75046	.	.	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000497673;ENST00000475668	.	.	.	4.18	1.37	0.22104	.	2.011330	0.02571	N	0.097759	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	6.415	0.21712	0.3133:0.0:0.6867:0.0	.	.	.	.	X	89	.	ENSP00000373973:E89X	E	+	1	0	MGAM	141354912	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.118000	0.15605	0.302000	0.22762	0.655000	0.94253	GAA		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			7	54	1	0	2.52707e-12	1	2.98654e-12	7	54				
ODAM	54959	broad.mit.edu	37	4	71062416	71062416	+	Missense_Mutation	SNP	C	C	G			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr4:71062416C>G	ENST00000396094.2	+	2	107	c.59C>G	c.(58-60)cCa>cGa	p.P20R		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	20					biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						TAGCTTATCCCACAGCGTCTC	0.333																																						ENST00000396094.2																			0				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						c.(58-60)cCa>cGa		odontogenic, ameloblast asssociated							69.0	62.0	64.0					4																	71062416		1824	4080	5904	SO:0001583	missense	54959				biomineral tissue development|odontogenesis of dentine-containing tooth	fibril		g.chr4:71062416C>G	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.59C>G	4.37:g.71062416C>G	ENSP00000379401:p.Pro20Arg						p.P20R	NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN			2	107	+			20					Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	37	c.59C>G	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428435	0.43122	.	.	ENSG00000109205	ENST00000396094	T	0.53423	0.62	5.39	5.39	0.77823	.	.	.	.	.	T	0.56601	0.1996	L	0.39898	1.24	0.80722	D	1	D	0.67145	0.996	P	0.62298	0.9	T	0.53858	-0.8379	9	0.48119	T	0.1	-3.6559	14.5147	0.67811	0.0:1.0:0.0:0.0	.	20	A1E959	ODAM_HUMAN	R	20	ENSP00000379401:P20R	ENSP00000379401:P20R	P	+	2	0	ODAM	71097005	0.984000	0.35163	0.951000	0.38953	0.210000	0.24377	3.347000	0.52200	2.804000	0.96469	0.650000	0.86243	CCA		0.333	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855		9	85	0	0	0	1	0	9	85				
ALG1L	200810	broad.mit.edu	37	3	125647387	125647387	+	IGR	SNP	G	G	A			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr3:125647387G>A	ENST00000340333.3	-	0	805				FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like								transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						ACCAGAAACTGTTTCCCTATG	0.502																																						ENST00000485843.1																			0																																																	SO:0001628	intergenic_variant	100125556							g.chr3:125647387G>A	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588		3.37:g.125647387G>A								NR_024251.1						0	532	+								D3DNA5	RNA	SNP	ENST00000340333.3	37		CCDS33840.1																																																																																				0.502	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050		5	152	0	0	0	1	0	5	152				
DNM1P47	100216544	broad.mit.edu	37	15	102304896	102304896	+	RNA	SNP	C	C	G			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr15:102304896C>G	ENST00000561463.1	+	0	12942									DNM1 pseudogene 47																		GAAGACACTCCTGGAGGAGTC	0.562																																						ENST00000561463.1																			0																																																			100216544							g.chr15:102304896C>G	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304896C>G														0	12942	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.562	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	26	0	0	0	1	0	3	26				
NBEAL2	23218	broad.mit.edu	37	3	47041446	47041446	+	Missense_Mutation	SNP	A	A	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr3:47041446A>T	ENST00000450053.3	+	27	4036	c.3857A>T	c.(3856-3858)gAt>gTt	p.D1286V	NBEAL2_ENST00000292309.5_Intron|NBEAL2_ENST00000383740.2_De_novo_Start_OutOfFrame	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1286					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GGCTGGCAAGATGTGCTGACC	0.632																																						ENST00000383740.2																			0				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51								neurobeachin-like 2							26.0	32.0	30.0					3																	47041446		2183	4284	6467	SO:0001583	missense	23218						binding	g.chr3:47041446A>T	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.3857A>T	3.37:g.47041446A>T	ENSP00000415034:p.Asp1286Val					NBEAL2_ENST00000292309.5_Intron|NBEAL2_ENST00000450053.3_Missense_Mutation_p.D1286V				Q6ZNJ1	NBEL2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)	0	4036	+		Acute lymphoblastic leukemia(5;0.0534)						O60288|Q6P994|Q6UX91|Q8NAC9	Translation_Start_Site	SNP	ENST00000450053.3	37		CCDS46817.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902208	0.72754	.	.	ENSG00000160796	ENST00000450053	T	0.62498	0.02	5.5	5.5	0.81552	.	.	.	.	.	T	0.74966	0.3786	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.77670	-0.2501	9	0.87932	D	0	.	13.5512	0.61734	1.0:0.0:0.0:0.0	.	1286	Q6ZNJ1	NBEL2_HUMAN	V	1286	ENSP00000415034:D1286V	ENSP00000415034:D1286V	D	+	2	0	NBEAL2	47016450	1.000000	0.71417	0.995000	0.50966	0.623000	0.37688	7.293000	0.78740	2.085000	0.62840	0.459000	0.35465	GAT		0.632	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		10	30	0	0	0	1	0	10	30				
TRBV6-5	28602	broad.mit.edu	37	7	142180979	142180979	+	RNA	SNP	C	C	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr7:142180979C>T	ENST00000390368.2	-	0	37									T cell receptor beta variable 6-5																		GAGGGGTCTTCTGTATCTGTG	0.602																																						ENST00000390368.2																			0																				52.0	58.0	56.0					7																	142180979		1954	4156	6110			28602							g.chr7:142180979C>T	L36092		7q34	2012-02-07			ENSG00000211721	ENSG00000211721		"""T cell receptors / TRB locus"""	12230	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV65, TCRBV13S1, TCRBV6S5			OTTHUMG00000158519		7.37:g.142180979C>T														0	37	-									RNA	SNP	ENST00000390368.2	37																																																																																						0.602	TRBV6-5-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000351225.1	NG_001333		4	40	0	0	0	1	0	4	40				
SIGLEC16	400709	broad.mit.edu	37	19	50473221	50473221	+	RNA	SNP	T	T	C	rs440731	byFrequency	TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr19:50473221T>C	ENST00000602139.1	+	0	222							A6NMB1	SIG16_HUMAN	sialic acid binding Ig-like lectin 16 (gene/pseudogene)						cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.W65R(3)		endometrium(2)|kidney(2)|lung(6)	10						GTTCAAAGGATGGACCAGCCC	0.602													T|||	728	0.145367	0.3162	0.049	5008	,	,		12105	0.128		0.0368	False		,,,				2504	0.1125					ENST00000602139.1																			3	Substitution - Missense(3)	p.W65R(3)	endometrium(2)|prostate(1)	endometrium(2)|kidney(2)|lung(6)	10								sialic acid binding Ig-like lectin 16 (gene/pseudogene)																																						400709							g.chr19:50473221T>C	BC030222		19q13.33	2014-03-20	2008-08-04	2008-08-04	ENSG00000161643	ENSG00000161643		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24851	protein-coding gene	gene with protein product			"""sialic acid binding Ig-like lectin, pseudogene 16"""	SIGLECP16		11986327, 18629938	Standard	NR_002825		Approved	Siglec-P16	uc002prf.3	A6NMB1	OTTHUMG00000183074		19.37:g.50473221T>C														0	222	+									RNA	SNP	ENST00000602139.1	37			.	.	.	.	.	.	.	.	.	.	T	0.001	-3.498236	0.00010	.	.	ENSG00000161643	ENST00000417280;ENST00000456956	.	.	.	1.92	-3.85	0.04243	.	1.955520	0.02343	N	0.075085	T	0.10594	0.0259	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.24584	-1.0156	5	0.06625	T	0.88	.	0.872	0.01216	0.1596:0.2304:0.3802:0.2299	rs440731	.	.	.	R	77;65	.	ENSP00000396157:W77R	W	+	1	0	SIGLEC16	55165033	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.343000	0.01099	-5.206000	0.00019	-3.107000	0.00063	TGG		0.602	SIGLEC16-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000464979.1	NR_002825		6	27	0	0	0	1	0	6	27				
HEPN1	641654	broad.mit.edu	37	11	124789688	124789688	+	Silent	SNP	C	C	T	rs368280630		TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr11:124789688C>T	ENST00000408930.5	+	1	543	c.42C>T	c.(40-42)ggC>ggT	p.G14G	HEPACAM_ENST00000298251.4_3'UTR	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1	14						cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		GGGTTGATGGCGAATCAGAGC	0.512																																						ENST00000408930.5																			0				large_intestine(1)|lung(1)|stomach(1)	3						c.(40-42)ggC>ggT		hepatocellular carcinoma, down-regulated 1							134.0	140.0	138.0					11																	124789688		2018	4183	6201	SO:0001819	synonymous_variant	641654					cytoplasm		g.chr11:124789688C>T	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"""cancer susceptibility gene HEPN1"""	611641	"""HEPACAM opposite strand 1"""			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939	ENST00000408930.5:c.42C>T	11.37:g.124789688C>T						HEPACAM_ENST00000298251.4_3'UTR	p.G14G	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)	1	543	+	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)	14						Silent	SNP	ENST00000408930.5	37	c.42C>T	CCDS41729.1																																																																																				0.512	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558		8	45	0	0	0	1	0	8	45				
ALG1L	200810	broad.mit.edu	37	3	125647396	125647396	+	IGR	SNP	T	T	C			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr3:125647396T>C	ENST00000340333.3	-	0	805				FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like								transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						TGTTTCCCTATGAAGAGCACT	0.502																																						ENST00000485843.1																			0																																																	SO:0001628	intergenic_variant	100125556							g.chr3:125647396T>C	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588		3.37:g.125647396T>C								NR_024251.1						0	541	+								D3DNA5	RNA	SNP	ENST00000340333.3	37		CCDS33840.1																																																																																				0.502	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050		6	154	0	0	0	1	0	6	154				
ING3	54556	broad.mit.edu	37	7	120607662	120607662	+	Silent	SNP	A	A	G			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr7:120607662A>G	ENST00000315870.5	+	7	664	c.516A>G	c.(514-516)ctA>ctG	p.L172L	ING3_ENST00000431467.1_Silent_p.L157L	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	172					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					AAGCTCTTCTATCCACCCTTA	0.303																																						ENST00000315870.5																			0				NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12						c.(514-516)ctA>ctG		inhibitor of growth family, member 3							78.0	83.0	82.0					7																	120607662		2203	4295	6498	SO:0001819	synonymous_variant	54556				histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding	g.chr7:120607662A>G	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"""Zinc fingers, PHD-type"""	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.516A>G	7.37:g.120607662A>G						ING3_ENST00000431467.1_Silent_p.L157L	p.L172L	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN			7	664	+	all_neural(327;0.117)		172					A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Silent	SNP	ENST00000315870.5	37	c.516A>G	CCDS5778.1																																																																																				0.303	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		51	146	0	0	0	1	0	51	146				
LDLRAD2	401944	broad.mit.edu	37	1	22142457	22142457	+	Missense_Mutation	SNP	G	G	A	rs373576797		TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr1:22142457G>A	ENST00000344642.2	+	3	720	c.533G>A	c.(532-534)cGc>cAc	p.R178H	LDLRAD2_ENST00000543870.1_Missense_Mutation_p.R178H	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN	low density lipoprotein receptor class A domain containing 2	178	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(3)	6		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)		GCCTACTTCCGCTGCCAGAAT	0.622																																						ENST00000344642.2																			0				endometrium(2)|large_intestine(1)|lung(3)	6						c.(532-534)cGc>cAc		low density lipoprotein receptor class A domain containing 2		G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	85.0	78.0	80.0		533	-1.5	0.8	1		80	0,8600		0,0,4300	no	missense	LDLRAD2	NM_001013693.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	178/273	22142457	1,13005	2203	4300	6503	SO:0001583	missense	401944					integral to membrane	receptor activity	g.chr1:22142457G>A	AL590103	CCDS30624.1	1p36.12	2008-02-05	2005-10-07		ENSG00000187942	ENSG00000187942			32071	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 2"""				Standard	NM_001013693		Approved		uc001bfg.1	Q5SZI1	OTTHUMG00000002675	ENST00000344642.2:c.533G>A	1.37:g.22142457G>A	ENSP00000340988:p.Arg178His					LDLRAD2_ENST00000543870.1_Missense_Mutation_p.R178H	p.R178H	NM_001013693.2	NP_001013715.2	Q5SZI1	LRAD2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;5.2e-26)|COAD - Colon adenocarcinoma(152;1.13e-05)|GBM - Glioblastoma multiforme(114;1.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00598)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	3	720	+		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.00166)|all_lung(284;0.00172)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)	178			LDL-receptor class A.		B9EJB3|Q6ZSN5	Missense_Mutation	SNP	ENST00000344642.2	37	c.533G>A	CCDS30624.1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.090065	0.36855	2.27E-4	0.0	ENSG00000187942	ENST00000344642;ENST00000543870	D;D	0.96136	-3.92;-3.92	4.29	-1.52	0.08637	.	1.045830	0.07567	N	0.917991	D	0.89072	0.6611	L	0.41356	1.27	0.25032	N	0.991268	B	0.29936	0.262	B	0.28849	0.095	T	0.77905	-0.2413	10	0.13853	T	0.58	-9.3861	1.2341	0.01949	0.2035:0.3268:0.3026:0.1671	.	178	Q5SZI1	LRAD2_HUMAN	H	178	ENSP00000340988:R178H;ENSP00000444097:R178H	ENSP00000340988:R178H	R	+	2	0	LDLRAD2	22015044	0.020000	0.18652	0.847000	0.33407	0.743000	0.42351	-0.686000	0.05161	0.082000	0.17018	-0.374000	0.07098	CGC		0.622	LDLRAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007601.1	NM_001013693		4	44	0	0	0	1	0	4	44				
ZNF773	374928	broad.mit.edu	37	19	58016080	58016080	+	Missense_Mutation	SNP	G	G	T			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr19:58016080G>T	ENST00000282292.4	+	2	229	c.89G>T	c.(88-90)aGa>aTa	p.R30I	ZNF773_ENST00000599847.1_Missense_Mutation_p.R30I|AC003005.4_ENST00000601674.1_3'UTR|ZNF773_ENST00000593916.1_Missense_Mutation_p.R29I|ZNF773_ENST00000598770.1_Missense_Mutation_p.R29I	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		GAGGAATGGAGATTGCTTGAT	0.532																																						ENST00000599847.1																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22						c.(88-90)aGa>aTa		zinc finger protein 773							179.0	153.0	162.0					19																	58016080		2203	4300	6503	SO:0001583	missense	374928				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:58016080G>T	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"""Zinc fingers, C2H2-type"", ""-"""	30487	protein-coding gene	gene with protein product			"""zinc finger protein 419B"""	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.89G>T	19.37:g.58016080G>T	ENSP00000282292:p.Arg30Ile					ZNF773_ENST00000282292.4_Missense_Mutation_p.R30I|AC003005.4_ENST00000601674.1_3'UTR|ZNF773_ENST00000593916.1_Missense_Mutation_p.R29I|ZNF773_ENST00000598770.1_Missense_Mutation_p.R29I	p.R30I			Q6PK81	ZN773_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)	2	231	+		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)	30			KRAB.		Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	c.89G>T	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095047	0.36952	.	.	ENSG00000152439	ENST00000332030;ENST00000282292	T	0.01838	4.61	1.39	0.261	0.15592	Krueppel-associated box (4);	.	.	.	.	T	0.04137	0.0115	L	0.56769	1.78	0.32365	N	0.556623	P;D	0.61080	0.666;0.989	B;P	0.52159	0.22;0.691	T	0.41342	-0.9514	9	0.44086	T	0.13	.	2.954	0.05870	0.1991:0.2917:0.5092:0.0	.	29;30	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	I	53;30	ENSP00000282292:R30I	ENSP00000282292:R30I	R	+	2	0	ZNF773	62707892	0.000000	0.05858	0.222000	0.23844	0.854000	0.48673	-0.485000	0.06520	0.147000	0.19030	0.305000	0.20034	AGA		0.532	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		5	125	1	0	0.184627	1	0.184627	5	125				
OR7E62P	26479	broad.mit.edu	37	2	71283122	71283123	+	RNA	INS	-	-	T	rs377557477|rs35074164|rs368732130	byFrequency	TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr2:71283122_71283123insT	ENST00000434990.1	-	0	61																											GGCACCACCCCCAGGAGTGGTG	0.53													?|-|T|unsure	814	0.16254	0.1286	0.1282	5008	,	,		19280	0.2272		0.0835	False		,,,				2504	0.2474					ENST00000434990.1																			0																																																			26479							g.chr2:71283122_71283123insT																													2.37:g.71283122_71283123insT														0	61	-									RNA	INS	ENST00000434990.1	37																																																																																						0.530	AC007040.8-001	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000332235.4			7	4						7	4	---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48866909	48866910	+	Frame_Shift_Ins	INS	-	-	T	rs537061158	byFrequency	TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr8:48866909_48866910insT	ENST00000314191.2	-	5	552_553	c.496_497insA	c.(496-498)atafs	p.I166fs	PRKDC_ENST00000338368.3_Frame_Shift_Ins_p.I166fs|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	166					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TGTATCTGGTATTTTTTTTTTC	0.267								Non-homologous end-joining																													Esophageal Squamous(79;1091 1253 12329 31680 40677)	ENST00000314191.2																			0				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147						c.(496-498)accfs	Non-homologous end-joining	protein kinase, DNA-activated, catalytic polypeptide																																				SO:0001589	frameshift_variant	5591				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding	g.chr8:48866909_48866910insT		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.497dupA	8.37:g.48866919_48866919dupT	ENSP00000313420:p.Ile166fs					PRKDC_ENST00000338368.3_Frame_Shift_Ins_p.T166fs|PRKDC_ENST00000523565.1_5'UTR	p.T166fs	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN			5	552_553	-		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)	166					P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Frame_Shift_Ins	INS	ENST00000314191.2	37	c.496_497insA																																																																																					0.267	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		2	4						2	4	---	---	---	---
BHLHE22	27319	broad.mit.edu	37	8	65493617	65493618	+	In_Frame_Ins	INS	-	-	GGC	rs544639534	byFrequency	TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr8:65493617_65493618insGGC	ENST00000321870.1	+	1	804_805	c.270_271insGGC	c.(271-273)ggc>GGCggc	p.91_91G>GG	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	91	Gly-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						gcgcgggaagtggcggcggcgg	0.782														385	0.076877	0.1475	0.0634	5008	,	,		7150	0.005		0.1223	False		,,,				2504	0.0184				Colon(113;104 1586 2865 9855 18065)	ENST00000321870.1																			0				NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						c.(268-273)aggcgg>agGGCgcgg		basic helix-loop-helix family, member e22																																				SO:0001652	inframe_insertion	27319				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr8:65493617_65493618insGGC	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"""Basic helix-loop-helix proteins"""	11963	protein-coding gene	gene with protein product		613483	"""trinucleotide repeat containing 20"", ""basic helix-loop-helix domain containing, class B, 5"""	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.286_288dupGGC	8.37:g.65493624_65493626dupGGC	ENSP00000318799:p.Gly97dup					RP11-21C4.1_ENST00000517909.1_RNA	p.90_91RR>RAR	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN			1	804_805	+			90			Gly-rich.			In_Frame_Ins	INS	ENST00000321870.1	37	c.270_271insGGC	CCDS6179.1																																																																																				0.782	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414		2	4						2	4	---	---	---	---
TRAV9-1	28678	broad.mit.edu	37	14	22279845	22279846	+	RNA	INS	-	-	T	rs374555375		TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr14:22279845_22279846insT	ENST00000390431.3	+	0	46									T cell receptor alpha variable 9-1																		TAATTTGTTTATTTTTTTTTCA	0.406																																						ENST00000390431.3																			0																																																			28678							g.chr14:22279845_22279846insT	AE000659		14q11.2	2012-02-07			ENSG00000211783	ENSG00000211783		"""T cell receptors / TRA locus"""	12153	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000168987		14.37:g.22279854_22279854dupT														0	46	+									RNA	INS	ENST00000390431.3	37																																																																																						0.406	TRAV9-1-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000401885.1	NG_001332		4	8						4	8	---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17720609	17720609	+	Frame_Shift_Del	DEL	G	G	-			TCGA-QR-A70R-01A-11D-A35D-08	TCGA-QR-A70R-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bf81a264-33bd-46bd-b03c-7c4537ee09e5	98d97958-f30c-438c-8f84-9d556fce7477	g.chr17:17720609delG	ENST00000261646.5	-	8	1751	c.1567delC	c.(1567-1569)catfs	p.H523fs	SREBF1_ENST00000395757.1_Frame_Shift_Del_p.H269fs|SREBF1_ENST00000355815.4_Frame_Shift_Del_p.H553fs|SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000338854.5_Frame_Shift_Del_p.H523fs	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	523					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						CCAGGGCTATGGTAGACGCTG	0.677																																						ENST00000355815.4																			0				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						c.(1657-1659)atfs		sterol regulatory element binding transcription factor 1							17.0	19.0	18.0					17																	17720609		2194	4289	6483	SO:0001589	frameshift_variant	6720				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding	g.chr17:17720609delG	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"""Basic helix-loop-helix proteins"""	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.1567delC	17.37:g.17720609delG	ENSP00000261646:p.His523fs					SREBF1_ENST00000338854.5_Frame_Shift_Del_p.H523fs|SREBF1_ENST00000395757.1_Frame_Shift_Del_p.H269fs|SREBF1_ENST00000261646.5_Frame_Shift_Del_p.H523fs	p.H553fs	NM_001005291.2	NP_001005291.1	P36956	SRBP1_HUMAN			9	1826	-			523					B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Frame_Shift_Del	DEL	ENST00000261646.5	37	c.1657delC	CCDS11189.1																																																																																				0.677	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		3	3						3	3	---	---	---	---
