#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
SORCS3	22986	broad.mit.edu	37	10	106918737	106918737	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:106918737C>A	ENST00000369701.3	+	11	1944	c.1717C>A	c.(1717-1719)Ctt>Att	p.L573I		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	573					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)		AGCCCCAGGACTTGTGGTGGC	0.433																																					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.(1717-1719)Ctt>Att		sortilin-related VPS10 domain containing receptor 3							87.0	79.0	82.0					10																	106918737		2203	4300	6503	SO:0001583	missense	22986					integral to membrane	neuropeptide receptor activity	g.chr10:106918737C>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.1717C>A	10.37:g.106918737C>A	ENSP00000358715:p.Leu573Ile						p.L573I	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)	11	1944	+		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)	573					Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	c.1717C>A	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.415625	0.25552	.	.	ENSG00000156395	ENST00000369701;ENST00000393176	T;T	0.57273	0.41;0.41	5.77	3.92	0.45320	VPS10 (1);	0.125004	0.56097	D	0.000037	T	0.30479	0.0766	N	0.10664	0.02	0.45216	D	0.998226	B	0.16166	0.016	B	0.18263	0.021	T	0.05402	-1.0887	9	.	.	.	.	12.4007	0.55412	0.0:0.8641:0.0:0.1359	.	573	Q9UPU3	SORC3_HUMAN	I	573;18	ENSP00000358715:L573I;ENSP00000376876:L18I	.	L	+	1	0	SORCS3	106908727	0.820000	0.29190	0.995000	0.50966	0.999000	0.98932	1.484000	0.35508	0.904000	0.36572	0.650000	0.86243	CTT		0.433	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		66	293	1	0	7.05995e-25	1	7.6875e-25	66	293				
FRG1B	284802	broad.mit.edu	37	20	29625875	29625875	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr20:29625875T>C	ENST00000278882.3	+	5	499	c.119T>C	c.(118-120)aTc>aCc	p.I40T	FRG1B_ENST00000358464.4_Missense_Mutation_p.I40T|FRG1B_ENST00000439954.2_Missense_Mutation_p.I45T			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	40								p.I40T(4)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGTACAGAATCGCCCTGAAA	0.358																																						ENST00000278882.3																			4	Substitution - Missense(4)	p.I40T(4)	prostate(4)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(118-120)aTc>aCc																																						SO:0001583	missense	0							g.chr20:29625875T>C			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.119T>C	20.37:g.29625875T>C	ENSP00000278882:p.Ile40Thr					FRG1B_ENST00000358464.4_Missense_Mutation_p.I40T|FRG1B_ENST00000439954.2_Missense_Mutation_p.I45T	p.I40T							5	499	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.119T>C		.	.	.	.	.	.	.	.	.	.	t	10.51	1.369778	0.24771	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.51071	0.72	1.68	1.68	0.24146	.	0.052751	0.64402	D	0.000001	T	0.59865	0.2225	.	.	.	0.51482	D	0.999924	P	0.49862	0.929	D	0.64687	0.928	T	0.59386	-0.7464	9	0.52906	T	0.07	.	7.3757	0.26827	0.0:0.0:0.0:1.0	.	45	F5H5R5	.	T	40;45;40	ENSP00000408863:I45T	ENSP00000278882:I40T	I	+	2	0	FRG1B	28239536	1.000000	0.71417	0.982000	0.44146	0.025000	0.11179	6.565000	0.73974	1.028000	0.39785	0.155000	0.16302	ATC		0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		20	483	0	0	0	1	0	20	483				
PAPPA2	60676	broad.mit.edu	37	1	176759114	176759114	+	Splice_Site	SNP	G	G	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:176759114G>C	ENST00000367662.3	+	18	6048		c.e18+1			NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2						bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						ACGTGAAAAGGTAAGGAACAT	0.418																																						ENST00000367662.3																			0				NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						c.e18+1		pappalysin 2							153.0	146.0	148.0					1																	176759114		1932	4136	6068	SO:0001630	splice_region_variant	60676				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding	g.chr1:176759114G>C	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4884+1G>C	1.37:g.176759114G>C								NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN			18	6048	+								A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Splice_Site	SNP	ENST00000367662.3	37		CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.156713	0.57259	.	.	ENSG00000116183	ENST00000367662	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6377	0.85063	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PAPPA2	175025737	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	6.533000	0.73829	2.651000	0.90000	0.650000	0.86243	.		0.418	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		Intron	129	517	0	0	0	1	0	129	517				
SEZ6L2	26470	broad.mit.edu	37	16	29908310	29908310	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:29908310G>T	ENST00000308713.5	-	3	871	c.344C>A	c.(343-345)gCa>gAa	p.A115E	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.A71E|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.A115E|SEZ6L2_ENST00000350527.3_Intron|SEZ6L2_ENST00000562159.1_5'UTR	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	115	Pro-rich.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTGGGGCCTGCCCCCCTGAC	0.736																																						ENST00000308713.5																			0				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(343-345)gCa>gAa		seizure related 6 homolog (mouse)-like 2							7.0	10.0	9.0					16																	29908310		2183	4256	6439	SO:0001583	missense	26470					endoplasmic reticulum membrane|integral to membrane|plasma membrane		g.chr16:29908310G>T	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.344C>A	16.37:g.29908310G>T	ENSP00000312550:p.Ala115Glu					SEZ6L2_ENST00000346932.5_Missense_Mutation_p.A115E|SEZ6L2_ENST00000350527.3_Intron|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.A71E|SEZ6L2_ENST00000562159.1_5'UTR	p.A115E	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN			3	871	-			115			Pro-rich.		B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	c.344C>A	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546087	0.65198	.	.	ENSG00000174938	ENST00000308713;ENST00000346932;ENST00000537485	T;T;T	0.44083	0.93;0.93;0.93	5.36	5.36	0.76844	.	0.123614	0.36374	N	0.002633	T	0.26231	0.0640	N	0.19112	0.55	0.31331	N	0.684786	B;B;B;B	0.33238	0.403;0.281;0.281;0.281	B;B;B;B	0.30855	0.121;0.057;0.104;0.057	T	0.24154	-1.0168	9	.	.	.	.	11.3559	0.49615	0.0844:0.0:0.9156:0.0	.	71;115;115;115	F5H293;B7Z5L4;Q9BW82;Q6UXD5	.;.;.;SE6L2_HUMAN	E	115;115;71	ENSP00000312550:A115E;ENSP00000319215:A115E;ENSP00000439412:A71E	.	A	-	2	0	SEZ6L2	29815811	0.445000	0.25657	1.000000	0.80357	0.965000	0.64279	3.770000	0.55310	2.523000	0.85059	0.561000	0.74099	GCA		0.736	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		4	48	1	0	0.000602214	1	0.000608423	4	48				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		9	216	0	0	0	1	0	9	216				
CYP4F22	126410	broad.mit.edu	37	19	15651359	15651359	+	Missense_Mutation	SNP	G	G	A	rs200005567		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:15651359G>A	ENST00000269703.3	+	8	969	c.770G>A	c.(769-771)cGc>cAc	p.R257H	CYP4F22_ENST00000601005.2_Missense_Mutation_p.R257H	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	257						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						ATTTACTACCGCTCGGCGGAT	0.582																																						ENST00000269703.2																			0				endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						c.(769-771)cGc>cAc		cytochrome P450, family 4, subfamily F, polypeptide 22		G	HIS/ARG	0,4406		0,0,2203	75.0	70.0	72.0		770	-6.8	0.0	19		72	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CYP4F22	NM_173483.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	257/532	15651359	1,13005	2203	4300	6503	SO:0001583	missense	126410					endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	g.chr19:15651359G>A		CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"""Cytochrome P450s"""	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.770G>A	19.37:g.15651359G>A	ENSP00000269703:p.Arg257His					CYP4F22_ENST00000601005.2_Missense_Mutation_p.R257H	p.R257H	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN			8	969	+			257					Q8N8H4	Missense_Mutation	SNP	ENST00000269703.3	37	c.770G>A	CCDS12331.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274344	0.23307	0.0	1.16E-4	ENSG00000171954	ENST00000269703	T	0.68765	-0.35	5.39	-6.85	0.01681	.	0.385586	0.27406	N	0.019502	T	0.55609	0.1931	L	0.45228	1.405	0.22511	N	0.999039	B	0.09022	0.002	B	0.08055	0.003	T	0.11060	-1.0603	10	0.62326	D	0.03	.	19.8166	0.96571	0.0:0.0:0.1486:0.8514	.	257	Q6NT55	CP4FN_HUMAN	H	257	ENSP00000269703:R257H	ENSP00000269703:R257H	R	+	2	0	CYP4F22	15512359	0.063000	0.20901	0.001000	0.08648	0.004000	0.04260	0.258000	0.18387	-1.590000	0.01623	0.453000	0.30009	CGC		0.582	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		202	282	0	0	0	1	0	202	282				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	26	345	0	0	0	1	0	26	345				
MROH7	374977	broad.mit.edu	37	1	55148429	55148429	+	Missense_Mutation	SNP	G	G	A	rs367669775		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:55148429G>A	ENST00000421030.2	+	14	2767	c.2482G>A	c.(2482-2484)Gtc>Atc	p.V828I	MROH7_ENST00000339553.5_Missense_Mutation_p.V828I|MROH7_ENST00000454855.2_Missense_Mutation_p.V346I|MROH7_ENST00000545244.1_Missense_Mutation_p.V396I|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.V828I|MROH7_ENST00000409996.1_Missense_Mutation_p.V396I|MROH7_ENST00000395690.2_Missense_Mutation_p.V828I	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	828						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GGAGAAGCCCGTCACCAAGGA	0.622																																						ENST00000414150.2																			0											c.(2482-2484)Gtc>Atc		maestro heat-like repeat family member 7		A	ILE/VAL	0,4046		0,0,2023	54.0	56.0	55.0		2482	2.3	0.8	1		55	1,8369		0,1,4184	no	missense	HEATR8	NM_001039464.2	29	0,1,6207	AA,AG,GG		0.0119,0.0,0.0081	benign	828/1324	55148429	1,12415	2023	4185	6208	SO:0001583	missense	374977							g.chr1:55148429G>A	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.2482G>A	1.37:g.55148429G>A	ENSP00000396622:p.Val828Ile					MROH7_ENST00000454855.2_Missense_Mutation_p.V346I|MROH7_ENST00000421030.2_Missense_Mutation_p.V828I|MROH7_ENST00000395690.2_Missense_Mutation_p.V828I|MROH7_ENST00000339553.5_Missense_Mutation_p.V828I|MROH7_ENST00000545244.1_Missense_Mutation_p.V396I|MROH7_ENST00000409996.1_Missense_Mutation_p.V396I	p.V828I							14	2760	+								A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	c.2482G>A	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	g	7.100	0.573946	0.13623	0.0	1.19E-4	ENSG00000184313	ENST00000421030;ENST00000545244;ENST00000414867;ENST00000339553;ENST00000409996;ENST00000454855;ENST00000395690	T;T;T;T;T;T	0.03982	4.79;3.74;4.24;4.54;4.42;4.24	4.25	2.34	0.29019	Armadillo-type fold (1);	0.753201	0.11320	N	0.576131	T	0.03348	0.0097	L	0.33485	1.01	0.09310	N	0.999993	B;B;B;B	0.33494	0.37;0.414;0.032;0.37	B;B;B;B	0.21708	0.036;0.023;0.008;0.033	T	0.45483	-0.9258	10	0.25106	T	0.35	-8.5791	5.4036	0.16308	0.1049:0.0:0.6974:0.1977	.	828;828;396;828	F8W8P2;Q68CQ1;F5H7R4;Q68CQ1-9	.;HEAT8_HUMAN;.;.	I	828;396;857;828;396;346;828	ENSP00000396622:V828I;ENSP00000442333:V396I;ENSP00000343211:V828I;ENSP00000387048:V396I;ENSP00000401130:V346I;ENSP00000379044:V828I	ENSP00000343211:V828I	V	+	1	0	HEATR8	54921017	0.196000	0.23350	0.753000	0.31225	0.254000	0.26022	0.258000	0.18387	0.529000	0.28599	-0.355000	0.07637	GTC		0.622	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		66	200	0	0	0	1	0	66	200				
NUAK1	9891	broad.mit.edu	37	12	106460608	106460608	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:106460608G>A	ENST00000261402.2	-	7	3337	c.1958C>T	c.(1957-1959)gCg>gTg	p.A653V		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	653					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GATCTCCAGCGCTTGCTTGTA	0.632																																						ENST00000261402.2																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						c.(1957-1959)gCg>gTg		NUAK family, SNF1-like kinase, 1							87.0	91.0	89.0					12																	106460608		2203	4300	6503	SO:0001583	missense	9891						ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr12:106460608G>A	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1958C>T	12.37:g.106460608G>A	ENSP00000261402:p.Ala653Val						p.A653V	NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN			7	3337	-			653					A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	c.1958C>T	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203470	0.95033	.	.	ENSG00000074590	ENST00000261402	D	0.82984	-1.67	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000012	D	0.90916	0.7145	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	D	0.91082	0.4900	10	0.87932	D	0	.	20.0609	0.97674	0.0:0.0:1.0:0.0	.	653	O60285	NUAK1_HUMAN	V	653	ENSP00000261402:A653V	ENSP00000261402:A653V	A	-	2	0	NUAK1	104984738	1.000000	0.71417	0.992000	0.48379	0.945000	0.59286	9.476000	0.97823	2.755000	0.94549	0.655000	0.94253	GCG		0.632	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		187	516	0	0	0	1	0	187	516				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382578.1_Silent_p.S281S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		13	325	0	0	0	1	0	13	325				
PLEKHH1	57475	broad.mit.edu	37	14	68044761	68044761	+	Missense_Mutation	SNP	G	G	A	rs201045091		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:68044761G>A	ENST00000329153.5	+	19	2728	c.2596G>A	c.(2596-2598)Gtg>Atg	p.V866M	PLEKHH1_ENST00000417684.2_5'Flank	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	866	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.					cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CTTCATCAACGTGCCGGTGGA	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19378	0.0		0.0	False		,,,				2504	0.0					ENST00000329153.5																			0				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19						c.(2596-2598)Gtg>Atg		pleckstrin homology domain containing, family H (with MyTH4 domain) member 1							77.0	79.0	78.0					14																	68044761		2167	4273	6440	SO:0001583	missense	57475					cytoskeleton	binding	g.chr14:68044761G>A	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.2596G>A	14.37:g.68044761G>A	ENSP00000330278:p.Val866Met						p.V866M	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN		all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)	19	2728	+			866			MyTH4.		A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	c.2596G>A	CCDS45128.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	28.8	4.949389	0.92660	.	.	ENSG00000054690	ENST00000329153	T	0.73789	-0.78	5.14	5.14	0.70334	MyTH4 domain (2);	0.000000	0.85682	D	0.000000	D	0.85647	0.5745	M	0.75264	2.295	0.80722	D	1	D	0.69078	0.997	D	0.66351	0.943	D	0.86972	0.2098	10	0.72032	D	0.01	.	18.7908	0.91973	0.0:0.0:1.0:0.0	.	866	Q9ULM0	PKHH1_HUMAN	M	866	ENSP00000330278:V866M	ENSP00000330278:V866M	V	+	1	0	PLEKHH1	67114514	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.257000	0.95545	2.665000	0.90641	0.655000	0.94253	GTG		0.597	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		181	324	0	0	0	1	0	181	324				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		12	331	0	0	0	1	0	12	331				
ANKHD1	54882	broad.mit.edu	37	5	139918629	139918629	+	Silent	SNP	A	A	G			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:139918629A>G	ENST00000360839.2	+	33	7684	c.7530A>G	c.(7528-7530)aaA>aaG	p.K2510K	ANKHD1_ENST00000297183.6_Silent_p.K2510K|ANKHD1_ENST00000544120.1_Silent_p.K834K|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.K2510K	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2510						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTATGATAAAAGTTATCCAAA	0.403																																						ENST00000297183.6																			0				breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60						c.(7528-7530)aaA>aaG		ankyrin repeat and KH domain containing 1							83.0	81.0	81.0					5																	139918629		2203	4300	6503	SO:0001819	synonymous_variant	54882							g.chr5:139918629A>G	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.7530A>G	5.37:g.139918629A>G						ANKHD1_ENST00000360839.2_Silent_p.K2510K|ANKHD1_ENST00000544120.1_Silent_p.K834K|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.K2510K	p.K2510K	NM_020690.5	NP_065741.3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		33	7654	+								A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	c.7530A>G	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.539|4.539	0.100145|0.100145	0.08731|0.08731	.|.	.|.	ENSG00000131503|ENSG00000131503	ENST00000421706|ENST00000435794;ENST00000432301	T|.	0.59638|.	0.25|.	5.87|5.87	4.73|4.73	0.59995|0.59995	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59445|0.59445	0.2194|0.2194	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57619|0.57619	-0.7780|-0.7780	7|4	0.87932|.	D|.	0|.	.|.	8.6414|8.6414	0.33978|0.33978	0.8578:0.0:0.1422:0.0|0.8578:0.0:0.1422:0.0	.|.	.|.	.|.	.|.	R|G	168|992;902	ENSP00000405345:K168R|.	ENSP00000405345:K168R|.	K|S	+|+	2|1	0|0	ANKHD1|ANKHD1	139898813|139898813	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.347000|2.347000	0.44036|0.44036	2.244000|2.244000	0.73946|0.73946	0.533000|0.533000	0.62120|0.62120	AAG|AGT		0.403	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		73	278	0	0	0	1	0	73	278				
PLEKHA3	65977	broad.mit.edu	37	2	179368599	179368599	+	Silent	SNP	A	A	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:179368599A>T	ENST00000234453.5	+	8	1290	c.888A>T	c.(886-888)ccA>ccT	p.P296P		NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	296						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			ATACTCTTCCATCCTTCTCTT	0.363																																						ENST00000234453.4																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11						c.(886-888)ccA>ccT		pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							72.0	73.0	72.0					2																	179368599		2202	4300	6502	SO:0001819	synonymous_variant	65977					cytoplasm|membrane		g.chr2:179368599A>T	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.888A>T	2.37:g.179368599A>T							p.P296P	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)		8	1290	+			296					Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	37	c.888A>T	CCDS33336.1																																																																																				0.363	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		53	307	0	0	0	1	0	53	307				
SLC12A6	9990	broad.mit.edu	37	15	34546711	34546711	+	Missense_Mutation	SNP	C	C	T	rs369334993		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:34546711C>T	ENST00000354181.3	-	9	1448	c.956G>A	c.(955-957)cGt>cAt	p.R319H	SLC12A6_ENST00000558667.1_Missense_Mutation_p.R319H|SLC12A6_ENST00000560164.1_Missense_Mutation_p.R131H|SLC12A6_ENST00000451844.2_Missense_Mutation_p.R131H|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000558589.1_Missense_Mutation_p.R310H|SLC12A6_ENST00000397702.2_Missense_Mutation_p.R260H|SLC12A6_ENST00000458406.2_Missense_Mutation_p.R260H|SLC12A6_ENST00000560611.1_Missense_Mutation_p.R319H|SLC12A6_ENST00000290209.5_Missense_Mutation_p.R268H|SLC12A6_ENST00000397707.2_Missense_Mutation_p.R304H			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	319					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GCCGTAGACACGCATGTTATT	0.453																																						ENST00000354181.3																			0				central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45						c.(955-957)cGt>cAt		solute carrier family 12 (potassium/chloride transporter), member 6	Potassium Chloride(DB00761)	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	142.0	124.0	130.0		779,779,929,911,803,956	5.1	1.0	15		130	0,8596		0,0,4298	no	missense,missense,missense,missense,missense,missense	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	29,29,29,29,29,29	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	260/1092,260/1092,310/1142,304/1136,268/1100,319/1151	34546711	1,12997	2201	4298	6499	SO:0001583	missense	9990				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity	g.chr15:34546711C>T	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.956G>A	15.37:g.34546711C>T	ENSP00000346112:p.Arg319His					SLC12A6_ENST00000558589.1_Missense_Mutation_p.R310H|SLC12A6_ENST00000558667.1_Missense_Mutation_p.R319H|SLC12A6_ENST00000458406.2_Missense_Mutation_p.R260H|SLC12A6_ENST00000397702.2_Missense_Mutation_p.R260H|SLC12A6_ENST00000397707.2_Missense_Mutation_p.R304H|SLC12A6_ENST00000451844.2_Missense_Mutation_p.R131H|SLC12A6_ENST00000290209.5_Missense_Mutation_p.R268H|SLC12A6_ENST00000560164.1_Missense_Mutation_p.R131H|SLC12A6_ENST00000560611.1_Missense_Mutation_p.R319H	p.R319H			Q9UHW9	S12A6_HUMAN		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	9	1448	-		all_lung(180;2.78e-08)	319					A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	c.956G>A	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	35	5.421433	0.96111	2.27E-4	0.0	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.86366	-2.1;-2.11;-2.11;-2.11;-1.59	5.1	5.1	0.69264	Amino acid permease domain (1);	0.063721	0.64402	N	0.000006	D	0.95601	0.8570	H	0.95402	3.665	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.993;0.999;1.0	D	0.96738	0.9544	10	0.87932	D	0	.	17.4519	0.87594	0.0:1.0:0.0:0.0	.	304;319;268;131	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	H	268;304;310;260;260;131	ENSP00000290209:R268H;ENSP00000380819:R304H;ENSP00000380814:R260H;ENSP00000387725:R260H;ENSP00000390199:R131H	ENSP00000290209:R268H	R	-	2	0	SLC12A6	32334003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.634000	0.89283	0.655000	0.94253	CGT		0.453	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		17	254	0	0	0	1	0	17	254				
POLR3B	55703	broad.mit.edu	37	12	106820987	106820987	+	Missense_Mutation	SNP	C	C	T	rs568917673		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:106820987C>T	ENST00000228347.4	+	13	1336	c.1114C>T	c.(1114-1116)Ctt>Ttt	p.L372F	POLR3B_ENST00000539066.1_Missense_Mutation_p.L314F|POLR3B_ENST00000549195.1_3'UTR	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	372					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.L372F(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						TTTATCTCTTCTTTTTGAAGA	0.274																																						ENST00000228347.4																			2	Substitution - Missense(2)	p.L372F(2)	urinary_tract(1)|prostate(1)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						c.(1114-1116)Ctt>Ttt		polymerase (RNA) III (DNA directed) polypeptide B																																				SO:0001583	missense	55703				innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding	g.chr12:106820987C>T	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1114C>T	12.37:g.106820987C>T	ENSP00000228347:p.Leu372Phe					POLR3B_ENST00000549195.1_3'UTR|POLR3B_ENST00000539066.1_Missense_Mutation_p.L314F	p.L372F	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN			13	1336	+			372					A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	c.1114C>T	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105377	0.77096	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066;ENST00000549569;ENST00000549195	T;T;T	0.79554	-0.26;-0.26;-1.28	5.62	4.73	0.59995	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	D	0.90157	0.6924	H	0.96142	3.775	0.80722	D	1	B	0.33964	0.434	P	0.47134	0.539	D	0.91279	0.5050	10	0.87932	D	0	-18.4128	11.6653	0.51370	0.0:0.8574:0.0:0.1426	.	372	Q9NW08	RPC2_HUMAN	F	372;372;314;130;35	ENSP00000228347:L372F;ENSP00000445721:L314F;ENSP00000448398:L130F	ENSP00000228347:L372F	L	+	1	0	POLR3B	105345117	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.535000	0.53575	1.506000	0.48736	0.557000	0.71058	CTT		0.274	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		12	82	0	0	0	1	0	12	82				
KHDRBS3	10656	broad.mit.edu	37	8	136594144	136594144	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:136594144G>A	ENST00000355849.5	+	6	1045	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	KHDRBS3_ENST00000520981.1_Intron	NM_006558.1	NP_006549.1	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal transduction associated 3	212	Interaction with SIAH1.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	26	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			GTTACAGCCCGGCCAGTTGGA	0.502																																						ENST00000355849.5																			0				NS(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	26						c.(634-636)cGg>cAg		KH domain containing, RNA binding, signal transduction associated 3							87.0	88.0	88.0					8																	136594144		2203	4300	6503	SO:0001583	missense	10656				regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding	g.chr8:136594144G>A	AF069681	CCDS6374.1	8q24.23	2008-05-15			ENSG00000131773	ENSG00000131773			18117	protein-coding gene	gene with protein product		610421				10332027, 10564820	Standard	XR_242372		Approved	T-STAR, Etle, etoile, SALP, SLM2, SLM-2	uc003yuv.3	O75525	OTTHUMG00000164164	ENST00000355849.5:c.635G>A	8.37:g.136594144G>A	ENSP00000348108:p.Arg212Gln					KHDRBS3_ENST00000520981.1_Intron	p.R212Q	NM_006558.1	NP_006549.1	O75525	KHDR3_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.247)		6	1045	+	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		212			Interaction with SIAH1.		Q6NUL8|Q9UPA8	Missense_Mutation	SNP	ENST00000355849.5	37	c.635G>A	CCDS6374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.81|15.81	2.942837|2.942837	0.53079|0.53079	.|.	.|.	ENSG00000131773|ENSG00000131773	ENST00000524282|ENST00000355849;ENST00000524199	.|T	.|0.45668	.|0.89	5.98|5.98	5.98|5.98	0.97165|0.97165	.|.	.|0.364746	.|0.32372	.|N	.|0.006188	T|T	0.34629|0.34629	0.0904|0.0904	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B;P	.|0.44816	.|0.431;0.844	.|B;B	.|0.37833	.|0.099;0.259	T|T	0.12400|0.12400	-1.0549|-1.0549	5|10	.|0.46703	.|T	.|0.11	-17.1845|-17.1845	14.227|14.227	0.65866|0.65866	0.0:0.2458:0.7542:0.0|0.0:0.2458:0.7542:0.0	.|.	.|212;212	.|O75525-2;O75525	.|.;KHDR3_HUMAN	S|Q	127|212;184	.|ENSP00000348108:R212Q	.|ENSP00000348108:R212Q	G|R	+|+	1|2	0|0	KHDRBS3|KHDRBS3	136663326|136663326	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.822000|0.822000	0.46500|0.46500	4.526000|4.526000	0.60566|0.60566	2.843000|2.843000	0.97960|0.97960	0.585000|0.585000	0.79938|0.79938	GGC|CGG		0.502	KHDRBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377529.1			84	524	0	0	0	1	0	84	524				
CEACAM3	1084	broad.mit.edu	37	19	42312866	42312866	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:42312866G>A	ENST00000357396.3	+	3	681	c.440G>A	c.(439-441)gGc>gAc	p.G147D	CEACAM3_ENST00000344550.4_Missense_Mutation_p.G147D|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.G147D	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	147						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						AATGCCCCAGGCCTTCCTGTG	0.612																																						ENST00000357396.3																			0				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						c.(439-441)gGc>gAc		carcinoembryonic antigen-related cell adhesion molecule 3							102.0	110.0	107.0					19																	42312866		2203	4300	6503	SO:0001583	missense	1084					integral to membrane		g.chr19:42312866G>A	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.440G>A	19.37:g.42312866G>A	ENSP00000349971:p.Gly147Asp					CEACAM3_ENST00000344550.4_Missense_Mutation_p.G147D|CEACAM3_ENST00000221999.4_Missense_Mutation_p.G147D|CEACAM3_ENST00000595255.1_3'UTR	p.G147D	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN			3	681	+			147					G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	37	c.440G>A	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	G	9.004	0.980901	0.18812	.	.	ENSG00000170956	ENST00000357396;ENST00000221999;ENST00000344550	T;T;T	0.01272	5.12;5.07;5.07	2.21	-1.96	0.07525	.	.	.	.	.	T	0.03348	0.0097	M	0.62088	1.915	0.09310	N	1	D;D	0.69078	0.995;0.997	D;D	0.68943	0.961;0.941	T	0.40403	-0.9565	9	0.17369	T	0.5	.	1.0058	0.01487	0.1539:0.2257:0.3909:0.2295	.	147;147	G5E978;P40198	.;CEAM3_HUMAN	D	147	ENSP00000349971:G147D;ENSP00000221999:G147D;ENSP00000341725:G147D	ENSP00000221999:G147D	G	+	2	0	CEACAM3	47004706	0.002000	0.14202	0.001000	0.08648	0.015000	0.08874	0.766000	0.26560	-0.299000	0.08909	0.514000	0.50259	GGC		0.612	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		401	805	0	0	0	1	0	401	805				
TTN	7273	broad.mit.edu	37	2	179537144	179537144	+	Silent	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:179537144G>A	ENST00000591111.1	-	150	34022	c.33798C>T	c.(33796-33798)ccC>ccT	p.P11266P	TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Silent_p.P11640P|TTN_ENST00000342992.6_Silent_p.P10339P|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11266	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTAGCTGGGGGAACAGCTT	0.338																																						ENST00000589042.1																			0				NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448						c.(34918-34920)ccC>ccT		titin							170.0	174.0	172.0					2																	179537144		1827	4074	5901	SO:0001819	synonymous_variant	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179537144G>A	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.33798C>T	2.37:g.179537144G>A						TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000591111.1_Silent_p.P11266P|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Silent_p.P10339P	p.P11640P	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		154	35144	-			11476			Glu-rich.|Pro-rich.		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37	c.34920C>T																																																																																					0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		483	813	0	0	0	1	0	483	813				
FAT1	2195	broad.mit.edu	37	4	187542860	187542860	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:187542860C>T	ENST00000441802.2	-	10	5089	c.4880G>A	c.(4879-4881)cGa>cAa	p.R1627Q		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1627	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTGGTTACTTCGATCTAATTC	0.368										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)	ENST00000441802.2																			0				NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						c.(4879-4881)cGa>cAa		FAT atypical cadherin 1							36.0	35.0	35.0					4																	187542860		1856	4087	5943	SO:0001583	missense	2195				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding	g.chr4:187542860C>T	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4880G>A	4.37:g.187542860C>T	ENSP00000406229:p.Arg1627Gln	HNSCC(5;0.00058)					p.R1627Q	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN			10	5089	-			1627			Cadherin 14.			Missense_Mutation	SNP	ENST00000441802.2	37	c.4880G>A	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.664646	0.29604	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01725	4.67	5.09	4.25	0.50352	Cadherin (4);Cadherin-like (1);	0.062767	0.64402	D	0.000004	T	0.02929	0.0087	M	0.76433	2.335	0.51482	D	0.999925	B	0.29590	0.25	B	0.23018	0.043	T	0.47341	-0.9125	10	0.27785	T	0.31	.	10.879	0.46927	0.0:0.8009:0.0:0.1991	.	1627	Q14517	FAT1_HUMAN	Q	1627;1629	ENSP00000406229:R1627Q	ENSP00000260147:R1629Q	R	-	2	0	FAT1	187779854	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.960000	0.40422	1.514000	0.48869	0.650000	0.86243	CGA		0.368	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		35	108	0	0	0	1	0	35	108				
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	A	rs121913530		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:25398285C>A	ENST00000256078.4	-	2	97	c.34G>T	c.(34-36)Ggt>Tgt	p.G12C	KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000311936.3_Missense_Mutation_p.G12C|KRAS_ENST00000557334.1_Missense_Mutation_p.G12C	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	ENST00000311936.3	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119		Dom	yes		12	12p12.1	3845	Mis	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog			"""L, E, M, O"""			"""pancreatic, colorectal, lung, thyroid, AML, others"""	UBE2L3/KRAS(2)	5144	Substitution - Missense(5142)|Insertion - In frame(2)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	GRCh37	CM076251	KRAS	M	rs121913530	c.(34-36)Ggt>Tgt		Kirsten rat sarcoma viral oncogene homolog							93.0	83.0	86.0					12																	25398285		2203	4300	6503	SO:0001583	missense	3845	Noonan syndrome;Cardiofaciocutaneous syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	g.chr12:25398285C>A	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>T	12.37:g.25398285C>A	ENSP00000256078:p.Gly12Cys	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				KRAS_ENST00000557334.1_Missense_Mutation_p.G12C|KRAS_ENST00000556131.1_Missense_Mutation_p.G12C|KRAS_ENST00000256078.4_Missense_Mutation_p.G12C	p.G12C	NM_004985.3	NP_004976.2	P01116	RASK_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		2	225	-	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		12		G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).			A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	c.34G>T	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676185	0.88445	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.91833	0.5477	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	C	12	ENSP00000308495:G12C;ENSP00000452512:G12C;ENSP00000256078:G12C;ENSP00000451856:G12C	ENSP00000256078:G12C	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		156	66	1	0	1.4734e-65	1	1.6597e-65	156	66				
ESPNP	284729	broad.mit.edu	37	1	17046613	17046613	+	RNA	SNP	C	C	T	rs3856294	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:17046613C>T	ENST00000492551.1	-	0	39					NR_026567.1				espin pseudogene																		CCAAAGCGGGCAGTCAGATGC	0.622													c|||	48	0.00958466	0.0325	0.0072	5008	,	,		41023	0.0		0.0	False		,,,				2504	0.0					ENST00000492551.1																			0																																																			0							g.chr1:17046613C>T	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17046613C>T								NR_026567.1						0	39	-									RNA	SNP	ENST00000492551.1	37																																																																																						0.622	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			12	312	0	0	0	1	0	12	312				
PIK3CG	5294	broad.mit.edu	37	7	106508944	106508944	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:106508944C>T	ENST00000359195.3	+	2	1248	c.938C>T	c.(937-939)cCg>cTg	p.P313L	PIK3CG_ENST00000440650.2_Missense_Mutation_p.P313L|PIK3CG_ENST00000496166.1_Missense_Mutation_p.P313L	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	313					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CCTCCAGACCCGGCCCTAGAC	0.587																																						ENST00000359195.3																			0				breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						c.(937-939)cCg>cTg		phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma							56.0	53.0	54.0					7																	106508944		2203	4300	6503	SO:0001583	missense	5294				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding	g.chr7:106508944C>T		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.938C>T	7.37:g.106508944C>T	ENSP00000352121:p.Pro313Leu					PIK3CG_ENST00000440650.2_Missense_Mutation_p.P313L|PIK3CG_ENST00000496166.1_Missense_Mutation_p.P313L	p.P313L	NM_002649.2	NP_002640.2	P48736	PK3CG_HUMAN			2	1248	+			313					A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	c.938C>T	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	C	4.728	0.135454	0.09032	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.68181	-0.31;-0.31;-0.31	5.75	5.75	0.90469	.	0.047482	0.85682	D	0.000000	T	0.62575	0.2439	L	0.48362	1.52	0.80722	D	1	B	0.13594	0.008	B	0.06405	0.002	T	0.55579	-0.8119	10	0.24483	T	0.36	-17.0025	19.9421	0.97168	0.0:1.0:0.0:0.0	.	313	P48736	PK3CG_HUMAN	L	313	ENSP00000392258:P313L;ENSP00000419260:P313L;ENSP00000352121:P313L	ENSP00000352121:P313L	P	+	2	0	PIK3CG	106296180	1.000000	0.71417	0.967000	0.41034	0.035000	0.12851	6.044000	0.71012	2.714000	0.92807	0.561000	0.74099	CCG		0.587	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			64	304	0	0	0	1	0	64	304				
TNXB	7148	broad.mit.edu	37	6	32038177	32038177	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:32038177C>T	ENST00000375244.3	-	14	5206	c.5005G>A	c.(5005-5007)Gcc>Acc	p.A1669T	TNXB_ENST00000375247.2_Missense_Mutation_p.A1669T			P22105	TENX_HUMAN	tenascin XB	1751	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCTGGGCTGGCGTCACCTCGG	0.607																																						ENST00000375244.3																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						c.(5005-5007)Gcc>Acc		tenascin XB							14.0	15.0	15.0					6																	32038177		1915	4096	6011	SO:0001583	missense	7148				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding	g.chr6:32038177C>T	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5005G>A	6.37:g.32038177C>T	ENSP00000364393:p.Ala1669Thr					TNXB_ENST00000375247.2_Missense_Mutation_p.A1669T	p.A1669T			P22105	TENX_HUMAN			14	5206	-			1751			Fibronectin type-III 9.		P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37	c.5005G>A		.	.	.	.	.	.	.	.	.	.	C	9.618	1.133059	0.21041	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.55760	0.66;0.5	4.87	0.759	0.18438	.	0.363230	0.20233	N	0.096454	T	0.08714	0.0216	N	0.17379	0.485	0.09310	N	1	P	0.37352	0.591	B	0.28385	0.089	T	0.28106	-1.0054	10	0.11182	T	0.66	.	4.8372	0.13471	0.1514:0.5711:0.0:0.2775	.	1669	P22105-3	.	T	1669	ENSP00000364393:A1669T;ENSP00000364396:A1669T	ENSP00000364393:A1669T	A	-	1	0	TNXB	32146155	0.028000	0.19301	0.707000	0.30419	0.942000	0.58702	-0.065000	0.11617	0.459000	0.27016	0.609000	0.83330	GCC		0.607	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		27	75	0	0	0	1	0	27	75				
TVP23C	201158	broad.mit.edu	37	17	15441469	15441469	+	Intron	SNP	C	C	T	rs568909748	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr17:15441469C>T	ENST00000225576.3	-	5	558				TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000583206.1_5'Flank|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000584811.1_Splice_Site|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Splice_Site	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)							integral component of membrane (GO:0016021)											TCCAGTGTTCCGCAAAAGACA	0.393													c|||	3	0.000599042	0.0015	0.0	5008	,	,		17476	0.001		0.0	False		,,,				2504	0.0					ENST00000584811.1																			0											c.e7-2		trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)																																				SO:0001627	intron_variant	201158							g.chr17:15441469C>T	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.462+7629G>A	17.37:g.15441469C>T						TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000225576.3_Intron|TVP23C_ENST00000428082.2_Splice_Site|TVP23C_ENST00000438826.3_Splice_Site								7	1815	-								Q3LIC7	Splice_Site	SNP	ENST00000225576.3	37		CCDS11170.1	.	.	.	.	.	.	.	.	.	.	c	13.58	2.280351	0.40294	.	.	ENSG00000175106	ENST00000438826	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0583	0.25111	0.0:0.1033:0.0:0.8967	.	.	.	.	.	-1	.	.	.	-	.	.	FAM18B2	15382194	1.000000	0.71417	0.996000	0.52242	0.698000	0.40448	1.919000	0.40015	0.852000	0.35287	-0.352000	0.07741	.		0.393	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		15	350	0	0	0	1	0	15	350				
NFRKB	4798	broad.mit.edu	37	11	129735831	129735831	+	Silent	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:129735831C>T	ENST00000446488.3	-	24	3682	c.3579G>A	c.(3577-3579)caG>caA	p.Q1193Q	NFRKB_ENST00000524794.1_Silent_p.Q1218Q|NFRKB_ENST00000524746.1_Silent_p.Q1193Q|NFRKB_ENST00000304521.5_Silent_p.Q1193Q	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1193					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CCTTCATTGGCTGGCTGATCA	0.498																																						ENST00000446488.3																			0				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32						c.(3577-3579)caG>caA		nuclear factor related to kappaB binding protein							134.0	114.0	121.0					11																	129735831		2201	4297	6498	SO:0001819	synonymous_variant	4798				DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding	g.chr11:129735831C>T		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3579G>A	11.37:g.129735831C>T						NFRKB_ENST00000524794.1_Silent_p.Q1218Q|NFRKB_ENST00000524746.1_Silent_p.Q1193Q|NFRKB_ENST00000304521.5_Silent_p.Q1193Q	p.Q1193Q	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)	24	3682	-	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)	1193					Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	c.3579G>A	CCDS44770.1																																																																																				0.498	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		52	330	0	0	0	1	0	52	330				
ZNF561	93134	broad.mit.edu	37	19	9727815	9727815	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:9727815G>C	ENST00000302851.3	-	4	510	c.147C>G	c.(145-147)gaC>gaG	p.D49E	ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000354661.4_5'UTR|ZNF561_ENST00000326044.5_Missense_Mutation_p.D49E|ZNF561_ENST00000424629.1_5'UTR	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	49	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(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						CTGGGGTGAAGTCCACAGCCA	0.463																																						ENST00000302851.3																			0				breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						c.(145-147)gaC>gaG		zinc finger protein 561							107.0	94.0	98.0					19																	9727815		692	1591	2283	SO:0001583	missense	93134				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:9727815G>C	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"""Zinc fingers, C2H2-type"", ""-"""	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.147C>G	19.37:g.9727815G>C	ENSP00000303915:p.Asp49Glu					ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000326044.5_Missense_Mutation_p.D49E|ZNF561_ENST00000424629.1_5'UTR|ZNF561_ENST00000354661.4_5'UTR	p.D49E	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN			4	510	-			49			KRAB.		B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	37	c.147C>G	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	G	0.191	-1.053706	0.01965	.	.	ENSG00000171469	ENST00000302851;ENST00000326044;ENST00000444611;ENST00000421525	T;T;T;T	0.01981	4.52;4.52;4.52;4.52	1.72	-0.904	0.10530	Krueppel-associated box (4);	.	.	.	.	T	0.01353	0.0044	N	0.11845	0.185	0.18873	N	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.46775	-0.9167	9	0.40728	T	0.16	.	3.7681	0.08630	0.0:0.2736:0.4482:0.2782	.	49	Q8N587	ZN561_HUMAN	E	49;49;55;49	ENSP00000303915:D49E;ENSP00000370284:D49E;ENSP00000392013:D55E;ENSP00000397599:D49E	ENSP00000303915:D49E	D	-	3	2	ZNF561	9588815	0.012000	0.17670	0.026000	0.17262	0.299000	0.27559	-1.203000	0.03019	-0.143000	0.11334	-0.834000	0.03071	GAC		0.463	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		11	293	0	0	0	1	0	11	293				
SLC30A1	7779	broad.mit.edu	37	1	211751575	211751575	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:211751575T>A	ENST00000367001.4	-	1	509	c.380A>T	c.(379-381)aAc>aTc	p.N127I		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	127					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		CCCCAGCACGTTGACCAGCAG	0.701																																						ENST00000367001.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11						c.(379-381)aAc>aTc		solute carrier family 30 (zinc transporter), member 1							16.0	19.0	18.0					1																	211751575		2195	4297	6492	SO:0001583	missense	7779				cadmium ion transmembrane transport|cellular calcium ion homeostasis|cellular zinc ion homeostasis|negative regulation of calcium ion import|negative regulation of neurotransmitter secretion|negative regulation of zinc ion import	integral to membrane|T-tubule	calcium channel inhibitor activity|zinc ion transmembrane transporter activity	g.chr1:211751575T>A	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"""Solute carriers"""	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.380A>T	1.37:g.211751575T>A	ENSP00000355968:p.Asn127Ile						p.N127I	NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)	1	509	-			127					Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	37	c.380A>T	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	T	34	5.391452	0.95988	.	.	ENSG00000170385	ENST00000367001	T	0.69685	-0.42	4.13	4.13	0.48395	.	0.048025	0.85682	D	0.000000	D	0.88043	0.6331	H	0.98646	4.29	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	D	0.92163	0.5737	10	0.87932	D	0	-13.1623	13.3232	0.60444	0.0:0.0:0.0:1.0	.	127	Q9Y6M5	ZNT1_HUMAN	I	127	ENSP00000355968:N127I	ENSP00000355968:N127I	N	-	2	0	SLC30A1	209818198	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.134000	0.77268	1.742000	0.51746	0.374000	0.22700	AAC		0.701	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			20	67	0	0	0	1	0	20	67				
COL22A1	169044	broad.mit.edu	37	8	139629165	139629165	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:139629165C>T	ENST00000303045.6	-	54	4308	c.3862G>A	c.(3862-3864)Ggt>Agt	p.G1288S	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.G1268S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1288	Collagen-like 12.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ACCCGGGGACCGGGTGCACCA	0.587										HNSCC(7;0.00092)																												ENST00000303045.6																			0				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211						c.(3862-3864)Ggt>Agt		collagen, type XXII, alpha 1							67.0	69.0	68.0					8																	139629165		2203	4300	6503	SO:0001583	missense	169044				cell adhesion	collagen|cytoplasm	structural molecule activity	g.chr8:139629165C>T	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3862G>A	8.37:g.139629165C>T	ENSP00000303153:p.Gly1288Ser	HNSCC(7;0.00092)				COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.G1268S	p.G1288S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0517)		54	4308	-	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		1288			Collagen-like 12.|Gly-rich.|Pro-rich.		B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	c.3862G>A	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.252523	0.39797	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99329	-5.75;-5.75	4.35	4.35	0.52113	.	0.281024	0.24791	N	0.035575	D	0.99704	0.9887	H	0.99634	4.67	0.48236	D	0.999613	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97160	0.9837	10	0.87932	D	0	.	12.6914	0.56976	0.0:1.0:0.0:0.0	.	1268;1288	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	S	1288;1268;981	ENSP00000303153:G1288S;ENSP00000387655:G1268S	ENSP00000303153:G1288S	G	-	1	0	COL22A1	139698347	0.997000	0.39634	0.990000	0.47175	0.154000	0.21943	3.554000	0.53720	2.709000	0.92574	0.555000	0.69702	GGT		0.587	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		79	411	0	0	0	1	0	79	411				
QARS	5859	broad.mit.edu	37	3	49136038	49136038	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:49136038C>A	ENST00000306125.6	-	20	2288	c.1951G>T	c.(1951-1953)Gtc>Ttc	p.V651F	QARS_ENST00000470225.1_5'Flank|QARS_ENST00000414533.1_Missense_Mutation_p.V640F			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	651					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	CTCACCTTGACAACATGCTGC	0.572																																						ENST00000306125.6																			0				breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19						c.(1951-1953)Gtc>Ttc		glutaminyl-tRNA synthetase	L-Glutamine(DB00130)						30.0	30.0	30.0					3																	49136038		2203	4300	6503	SO:0001583	missense	5859				glutaminyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|glutamine-tRNA ligase activity|protein binding	g.chr3:49136038C>A	X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"""Aminoacyl tRNA synthetases / Class I"""	9751	protein-coding gene	gene with protein product	"""glutamine tRNA ligase"""	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.1951G>T	3.37:g.49136038C>A	ENSP00000307567:p.Val651Phe					QARS_ENST00000414533.1_Missense_Mutation_p.V640F	p.V651F			P47897	SYQ_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	20	2288	-			651					B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	37	c.1951G>T	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.470300	0.43942	.	.	ENSG00000172053	ENST00000453392;ENST00000306125;ENST00000414533	T;T	0.24151	1.87;1.87	5.9	-0.927	0.10451	Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain (1);Ribosomal protein L25/Gln-tRNA synthetase, beta-barrel domain (1);Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain (1);	0.277142	0.39407	N	0.001378	T	0.39200	0.1069	M	0.89785	3.06	0.80722	D	1	B;B	0.30033	0.266;0.266	B;B	0.42882	0.401;0.401	T	0.26121	-1.0112	10	0.52906	T	0.07	-11.7339	6.1598	0.20358	0.0:0.3728:0.1329:0.4943	.	640;651	B4DWJ2;P47897	.;SYQ_HUMAN	F	171;651;640	ENSP00000307567:V651F;ENSP00000390015:V640F	ENSP00000307567:V651F	V	-	1	0	QARS	49111042	1.000000	0.71417	0.173000	0.22940	0.943000	0.58893	0.624000	0.24462	-0.084000	0.12595	-0.254000	0.11334	GTC		0.572	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		27	104	1	0	9.04412e-07	1	9.42898e-07	27	104				
RP11-156P1.3	0	broad.mit.edu	37	17	45128812	45128812	+	RNA	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr17:45128812C>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AGTCCTGTTTCTGTGTGGATT	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128812C>T																													17.37:g.45128812C>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			8	188	0	0	0	1	0	8	188				
COL5A1	1289	broad.mit.edu	37	9	137653805	137653805	+	Missense_Mutation	SNP	C	C	T	rs149912828	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:137653805C>T	ENST00000371817.3	+	19	2384	c.1970C>T	c.(1969-1971)cCg>cTg	p.P657L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	657	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCAGGACCTCCGGGAGACGAT	0.597																																						ENST00000371817.3																			0				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115						c.(1969-1971)cCg>cTg		collagen, type V, alpha 1			LEU/PRO	0,4404		0,0,2202	109.0	100.0	103.0		1970	4.5	0.6	9	dbSNP_134	103	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL5A1	NM_000093.3	98	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	657/1839	137653805	1,13003	2202	4300	6502	SO:0001583	missense	1289				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding	g.chr9:137653805C>T	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1970C>T	9.37:g.137653805C>T	ENSP00000360882:p.Pro657Leu						p.P657L	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)	19	2384	+		Myeloproliferative disorder(178;0.0341)	657			Triple-helical region.		Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	c.1970C>T	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	c	9.891	1.204150	0.22205	0.0	1.16E-4	ENSG00000130635	ENST00000371817	D	0.96685	-4.09	4.53	4.53	0.55603	.	0.152829	0.44688	U	0.000431	D	0.97835	0.9289	M	0.82823	2.61	0.51233	D	0.99991	D	0.89917	1.0	D	0.74023	0.982	D	0.98448	1.0590	10	0.87932	D	0	.	12.7642	0.57383	0.0:1.0:0.0:0.0	.	657	P20908	CO5A1_HUMAN	L	657	ENSP00000360882:P657L	ENSP00000360882:P657L	P	+	2	0	COL5A1	136793626	0.972000	0.33761	0.573000	0.28510	0.014000	0.08584	5.210000	0.65214	2.067000	0.61834	0.556000	0.70494	CCG		0.597	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		48	321	0	0	0	1	0	48	321				
SLC18A2	6571	broad.mit.edu	37	10	119029974	119029974	+	Splice_Site	SNP	G	G	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:119029974G>T	ENST00000298472.5	+	15	1583	c.1440G>T	c.(1438-1440)atG>atT	p.M480I	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	480					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AAGAAAAAATGGTAAGAAAAA	0.363																																						ENST00000298472.5																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29						c.e15+1		solute carrier family 18 (vesicular monoamine transporter), member 2	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)						82.0	80.0	81.0					10																	119029974		2203	4300	6503	SO:0001630	splice_region_variant	6571				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity	g.chr10:119029974G>T	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.1440+1G>T	10.37:g.119029974G>T						SLC18A2_ENST00000497497.1_3'UTR	p.M480_splice	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN		all cancers(201;0.029)	15	1583	+		Colorectal(252;0.19)	480					B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Splice_Site	SNP	ENST00000298472.5	37	c.1440_splice	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150787	0.37923	.	.	ENSG00000165646	ENST00000298472	T	0.03524	3.9	5.77	5.77	0.91146	.	0.041993	0.85682	D	0.000000	T	0.04227	0.0117	N	0.17723	0.515	0.54753	D	0.99998	B	0.02656	0.0	B	0.06405	0.002	T	0.53683	-0.8404	10	0.36615	T	0.2	-29.9914	19.9818	0.97329	0.0:0.0:1.0:0.0	.	480	Q05940	VMAT2_HUMAN	I	480	ENSP00000298472:M480I	ENSP00000298472:M480I	M	+	3	0	SLC18A2	119019964	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.576000	0.60915	2.717000	0.92951	0.462000	0.41574	ATG		0.363	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	Missense_Mutation	70	340	1	0	7.46257e-40	1	8.31059e-40	70	340				
ALDH16A1	126133	broad.mit.edu	37	19	49971707	49971707	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:49971707G>T	ENST00000293350.4	+	15	2171	c.2008G>T	c.(2008-2010)Gac>Tac	p.D670Y	ALDH16A1_ENST00000433981.2_Missense_Mutation_p.D505Y|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.D619Y|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.D507Y	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	670						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GGTGTGTCCGGACGAGTGGCC	0.697																																						ENST00000293350.4																			0				cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20						c.(2008-2010)Gac>Tac		aldehyde dehydrogenase 16 family, member A1							135.0	143.0	140.0					19																	49971707		2203	4299	6502	SO:0001583	missense	126133						oxidoreductase activity|protein binding	g.chr19:49971707G>T	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.2008G>T	19.37:g.49971707G>T	ENSP00000293350:p.Asp670Tyr					ALDH16A1_ENST00000540132.1_Missense_Mutation_p.D507Y|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.D619Y|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.D505Y	p.D670Y	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)	15	2171	+		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)	670					B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	c.2008G>T	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.324210	0.41197	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	4.89	4.89	0.63831	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.101073	0.64402	D	0.000004	D	0.83912	0.5357	M	0.68593	2.085	0.35738	D	0.818491	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.959;0.967;0.995	D	0.88296	0.2946	10	0.62326	D	0.03	-6.9053	13.9554	0.64144	0.0:0.0:1.0:0.0	.	507;619;670	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	Y	670;619;507;505	ENSP00000293350:D670Y;ENSP00000410142:D619Y;ENSP00000445088:D507Y;ENSP00000398675:D505Y	ENSP00000293350:D670Y	D	+	1	0	ALDH16A1	54663519	0.965000	0.33210	0.523000	0.27875	0.062000	0.15995	2.375000	0.44283	2.426000	0.82243	0.485000	0.47835	GAC		0.697	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		258	718	1	0	1.34946e-99	1	1.53776e-99	258	718				
BMS1P20	96610	broad.mit.edu	37	22	22661208	22661208	+	RNA	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:22661208C>T	ENST00000426066.1	+	0	300					NR_027293.1				BMS1 pseudogene 20																		CTGAATCATGCAGAATTTGAA	0.408																																						ENST00000426066.1																			0																																																			0							g.chr22:22661208C>T			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661208C>T								NR_027293.1						0	300	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.408	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			21	231	0	0	0	1	0	21	231				
ABCB1	5243	broad.mit.edu	37	7	87195527	87195527	+	Silent	SNP	A	A	G			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:87195527A>G	ENST00000265724.3	-	8	978	c.561T>C	c.(559-561)ggT>ggC	p.G187G	ABCB1_ENST00000543898.1_Silent_p.G123G	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	187	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CAATTTTGTCACCAATTCCTT	0.363																																						ENST00000265724.3																			0				NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111						c.(559-561)ggT>ggC		ATP-binding cassette, sub-family B (MDR/TAP), member 1	Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)						144.0	134.0	137.0					7																	87195527		2203	4300	6503	SO:0001819	synonymous_variant	5243				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity	g.chr7:87195527A>G	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.561T>C	7.37:g.87195527A>G						ABCB1_ENST00000543898.1_Silent_p.G123G	p.G187G	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN			8	978	-	Esophageal squamous(14;0.00164)		187			ABC transmembrane type-1 1.		A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	37	c.561T>C	CCDS5608.1																																																																																				0.363	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		91	401	0	0	0	1	0	91	401				
INSR	3643	broad.mit.edu	37	19	7117089	7117089	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:7117089A>C	ENST00000302850.5	-	22	4269	c.4127T>G	c.(4126-4128)tTg>tGg	p.L1376W	INSR_ENST00000341500.5_Missense_Mutation_p.L1364W	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1376					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	GGACCGAGGCAAGGTCAGAAT	0.567																																						ENST00000341500.5																			0				breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66						c.(4090-4092)tTg>tGg		insulin receptor	Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)						126.0	109.0	115.0					19																	7117089		2203	4300	6503	SO:0001583	missense	0				activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding	g.chr19:7117089A>C	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.4127T>G	19.37:g.7117089A>C	ENSP00000303830:p.Leu1376Trp					INSR_ENST00000302850.5_Missense_Mutation_p.L1376W	p.L1364W	NM_001079817.1	NP_001073285.1	P06213	INSR_HUMAN			21	4130	-			1376			PIK3R1-binding.		Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	c.4091T>G	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.320919	0.60634	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	T;T	0.79940	-1.32;-1.32	4.9	4.9	0.64082	.	0.205339	0.23828	N	0.044170	D	0.90058	0.6895	M	0.86651	2.83	0.44562	D	0.997526	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.986	D	0.91501	0.5219	10	0.87932	D	0	.	12.5167	0.56036	1.0:0.0:0.0:0.0	.	1364;1376	P06213-2;P06213	.;INSR_HUMAN	W	1376;1364	ENSP00000303830:L1376W;ENSP00000342838:L1364W	ENSP00000303830:L1376W	L	-	2	0	INSR	7068089	1.000000	0.71417	0.947000	0.38551	0.478000	0.33099	6.780000	0.75063	2.057000	0.61298	0.460000	0.39030	TTG		0.567	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			147	563	0	0	0	1	0	147	563				
HMMR	3161	broad.mit.edu	37	5	162901193	162901193	+	Silent	SNP	A	A	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:162901193A>T	ENST00000358715.3	+	10	1068	c.1032A>T	c.(1030-1032)tcA>tcT	p.S344S	HMMR_ENST00000393915.4_Silent_p.S345S|HMMR_ENST00000432118.2_Silent_p.S258S|HMMR_ENST00000353866.3_Silent_p.S329S			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	344					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AAATTGATTCACTTCTGCAAC	0.303																																						ENST00000416990.2																			0				cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23						c.(688-690)tcA>tcT		hyaluronan-mediated motility receptor (RHAMM)							72.0	72.0	72.0					5																	162901193		2202	4299	6501	SO:0001819	synonymous_variant	3161					cell surface|cytoplasm	hyaluronic acid binding	g.chr5:162901193A>T	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1032A>T	5.37:g.162901193A>T						HMMR_ENST00000393915.4_Silent_p.S345S|HMMR_ENST00000358715.3_Silent_p.S344S|HMMR_ENST00000432118.2_Silent_p.S258S|HMMR_ENST00000353866.3_Silent_p.S329S	p.S230S			O75330	HMMR_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	10	1187	+	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	344					A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Silent	SNP	ENST00000358715.3	37	c.690A>T	CCDS4362.1																																																																																				0.303	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		25	170	0	0	0	1	0	25	170				
FOXG1	2290	broad.mit.edu	37	14	29237195	29237195	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:29237195A>G	ENST00000313071.4	+	1	909	c.710A>G	c.(709-711)aAg>aGg	p.K237R	FOXG1_ENST00000382535.3_Missense_Mutation_p.K237R|RP11-966I7.1_ENST00000551395.1_RNA|RP11-966I7.1_ENST00000546560.1_RNA|RP11-966I7.1_ENST00000549487.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	237				K -> M (in Ref. 5; AAH50072). {ECO:0000305}.	aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		TCCCTCAACAAGTGCTTCGTG	0.587																																						ENST00000382535.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43						c.(709-711)aAg>aGg		forkhead box G1							48.0	48.0	48.0					14																	29237195		2203	4300	6503	SO:0001583	missense	2290				axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue 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.chr14:29237195A>G		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"""Forkhead boxes"""	3811	protein-coding gene	gene with protein product		164874	"""forkhead box G1B"", ""forkhead box G1C"", ""forkhead box G1A"""	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.710A>G	14.37:g.29237195A>G	ENSP00000339004:p.Lys237Arg					FOXG1_ENST00000313071.4_Missense_Mutation_p.K237R	p.K237R			P55316	FOXG1_HUMAN	LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)	2	1079	+			237	K -> M (in Ref. 5; AAH50072).				A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	37	c.710A>G	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561743	0.86335	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.96073	-3.9;-3.9	4.01	4.01	0.46588	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	U	0.000000	D	0.96664	0.8911	L	0.59912	1.85	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96908	0.9665	10	0.87932	D	0	.	12.6221	0.56610	1.0:0.0:0.0:0.0	.	237	P55316	FOXG1_HUMAN	R	237	ENSP00000371975:K237R;ENSP00000339004:K237R	ENSP00000339004:K237R	K	+	2	0	FOXG1	28306946	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.184000	0.94893	1.446000	0.47643	0.254000	0.18369	AAG		0.587	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			92	151	0	0	0	1	0	92	151				
SDHAP1	255812	broad.mit.edu	37	3	195711423	195711423	+	RNA	SNP	A	A	G	rs201502468		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:195711423A>G	ENST00000427841.1	-	0	524					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		CTCTTGTACTAGAAACAGACC	0.552																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195711423A>G	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195711423A>G								NR_003264.2						0	524	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.552	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			8	172	0	0	0	1	0	8	172				
CIC	23152	broad.mit.edu	37	19	42797190	42797190	+	Silent	SNP	C	C	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:42797190C>A	ENST00000575354.2	+	15	3592	c.3552C>A	c.(3550-3552)atC>atA	p.I1184I	CIC_ENST00000572681.2_Silent_p.I2091I|CIC_ENST00000160740.3_Silent_p.I1182I	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1184	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				AGGCAGCCATCGCCAGCATTC	0.662			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(6271-6273)atC>atA		capicua transcriptional repressor							20.0	23.0	22.0					19																	42797190		2178	4244	6422	SO:0001819	synonymous_variant	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42797190C>A	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3552C>A	19.37:g.42797190C>A						CIC_ENST00000160740.3_Silent_p.I1182I|CIC_ENST00000575354.2_Silent_p.I1184I	p.I2091I			Q96RK0	CIC_HUMAN			16	6341	+		Prostate(69;0.00682)	1184					Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	37	c.6273C>A	CCDS12601.1																																																																																				0.662	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			70	165	1	0	9.21137e-24	1	9.91993e-24	70	165				
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	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.S167S(19)		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)		tgctgctgctactgctgctgc	0.532			T	MLL	ALL								A|||	612	0.122204	0.1505	0.1066	5008	,	,		12422	0.0833		0.0716	False		,,,				2504	0.1871					ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		19	Substitution - coding silent(19)	p.S167S(19)	lung(8)|kidney(5)|endometrium(3)|central_nervous_system(1)|urinary_tract(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.(499-501)agT>agC		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414343		1537	3257	4794	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414343A>G	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.501T>C	9.37:g.20414343A>G						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	p.S167S	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	787	-			167			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.501T>C	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		13	229	0	0	0	1	0	13	229				
ANXA7	310	broad.mit.edu	37	10	75156930	75156930	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:75156930G>A	ENST00000372921.5	-	4	418	c.362C>T	c.(361-363)cCa>cTa	p.P121L	ANXA7_ENST00000492380.1_5'UTR|ANXA7_ENST00000535178.1_Intron	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	121	Repeat-rich region.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					ACCAGGTAGTGGAACCTGTGC	0.453																																						ENST00000372921.4																			0				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26						c.(361-363)cCa>cTa		annexin A7							61.0	52.0	55.0					10																	75156930		2203	4300	6503	SO:0001583	missense	310						calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding	g.chr10:75156930G>A	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.362C>T	10.37:g.75156930G>A	ENSP00000362012:p.Pro121Leu					ANXA7_ENST00000492380.1_5'UTR|ANXA7_ENST00000535178.1_Intron	p.P121L	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN			4	418	-	Prostate(51;0.0119)		121			Repeat-rich region.		Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	37	c.362C>T	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641575	0.47153	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000394847	T;T	0.02606	4.23;4.4	5.48	4.46	0.54185	.	1.044460	0.07552	N	0.915625	T	0.08582	0.0213	L	0.32530	0.975	0.80722	D	1	D;D;P	0.69078	0.975;0.997;0.935	P;P;P	0.61397	0.575;0.888;0.476	T	0.29305	-1.0016	10	0.49607	T	0.09	.	12.7479	0.57291	0.0:0.0:0.801:0.199	.	48;121;121	B4DWU2;P20073-2;P20073	.;.;ANXA7_HUMAN	L	121	ENSP00000362012:P121L;ENSP00000362010:P121L	ENSP00000362010:P121L	P	-	2	0	ANXA7	74826936	1.000000	0.71417	0.968000	0.41197	0.052000	0.14988	2.523000	0.45580	2.736000	0.93811	0.555000	0.69702	CCA		0.453	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		40	88	0	0	0	1	0	40	88				
LDLR	3949	broad.mit.edu	37	19	11242044	11242044	+	3'UTR	SNP	G	G	A	rs14158	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:11242044G>A	ENST00000558518.1	+	0	2822				LDLR_ENST00000557933.1_Silent_p.P899P|LDLR_ENST00000535915.1_3'UTR|LDLR_ENST00000560628.1_Intron|LDLR_ENST00000455727.2_3'UTR|LDLR_ENST00000545707.1_3'UTR|LDLR_ENST00000558013.1_3'UTR	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor						cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	AGACCTCGCCGGCCTTGTTTT	0.507											OREG0025249	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1170	0.233626	0.1551	0.219	5008	,	,		18237	0.4107		0.2266	False		,,,				2504	0.1748				GBM(18;201 575 7820 21545)	ENST00000557933.1																			0				breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(2695-2697)ccG>ccA		low density lipoprotein receptor	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	G	,,,,,	455,2199		42,371,914	105.0	98.0	100.0		,,,,,	-2.0	0.0	19	dbSNP_52	100	1123,3495		132,859,1318	no	utr-3,utr-3,utr-3,utr-3,utr-3,utr-3	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	174,1230,2232	AA,AG,GG		24.3179,17.1439,21.6997	,,,,,	,,,,,	11242044	1578,5694	1327	2309	3636	SO:0001624	3_prime_UTR_variant	3949				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity	g.chr19:11242044G>A	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.*52G>A	19.37:g.11242044G>A			OREG0025249	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	670	LDLR_ENST00000560628.1_Intron|LDLR_ENST00000545707.1_3'UTR|LDLR_ENST00000455727.2_3'UTR|LDLR_ENST00000558013.1_3'UTR|LDLR_ENST00000558518.1_3'UTR|LDLR_ENST00000535915.1_3'UTR	p.P899P			P01130	LDLR_HUMAN		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	18	2784	+		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)	0					B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	c.2697G>A	CCDS12254.1																																																																																				0.507	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			12	313	0	0	0	1	0	12	313				
FLRT2	23768	broad.mit.edu	37	14	86089365	86089365	+	Missense_Mutation	SNP	G	G	A	rs149005998		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:86089365G>A	ENST00000330753.4	+	2	2274	c.1507G>A	c.(1507-1509)Gcg>Acg	p.A503T	FLRT2_ENST00000554746.1_Missense_Mutation_p.A503T	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	503	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TAACTACCGCGCGGTAGAAGA	0.537																																						ENST00000330753.4																			0				NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73						c.(1507-1509)Gcg>Acg		fibronectin leucine rich transmembrane protein 2		G	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	131.0	119.0	123.0		1507	5.1	0.3	14	dbSNP_134	123	2,8598	2.2+/-6.3	0,2,4298	no	missense	FLRT2	NM_013231.4	58	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	benign	503/661	86089365	4,13002	2203	4300	6503	SO:0001583	missense	23768				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity	g.chr14:86089365G>A	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1507G>A	14.37:g.86089365G>A	ENSP00000332879:p.Ala503Thr					FLRT2_ENST00000554746.1_Missense_Mutation_p.A503T	p.A503T	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.0319)	2	2274	+			503			Fibronectin type-III.		A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	c.1507G>A	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	G	2.547	-0.304874	0.05495	4.54E-4	2.33E-4	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.55930	0.49;0.49	6.17	5.07	0.68467	Fibronectin, type III (1);	0.164767	0.56097	N	0.000039	T	0.39091	0.1065	L	0.38175	1.15	0.31348	N	0.682867	B	0.09022	0.002	B	0.04013	0.001	T	0.39375	-0.9617	10	0.13853	T	0.58	-6.2272	10.3338	0.43837	0.1995:0.0:0.8005:0.0	.	503	O43155	FLRT2_HUMAN	T	503;503;156	ENSP00000332879:A503T;ENSP00000451050:A503T	ENSP00000332879:A503T	A	+	1	0	FLRT2	85159118	1.000000	0.71417	0.302000	0.25058	0.145000	0.21501	4.224000	0.58593	1.277000	0.44412	0.655000	0.94253	GCG		0.537	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			311	481	0	0	0	1	0	311	481				
FUS	2521	broad.mit.edu	37	16	31200485	31200485	+	Silent	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:31200485C>T	ENST00000254108.7	+	9	979	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	FUS_ENST00000380244.3_Silent_p.L291L|FUS_ENST00000568685.1_Silent_p.L293L|FUS_ENST00000474990.1_3'UTR	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	292	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TGTGCAAGGCCTGGGTGAGAA	0.388			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																	ENST00000254108.7				Dom	yes		16	16p11.2	2521	T	"""fusion, derived from t(12;16) malignant liposarcoma"""			"""M, L"""	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""		"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""	FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	0				breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22						c.(874-876)Ctg>Ttg		fused in sarcoma							287.0	260.0	269.0					16																	31200485		2197	4300	6497	SO:0001819	synonymous_variant	2521				cell death|nuclear mRNA splicing, via spliceosome	nucleoplasm	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding	g.chr16:31200485C>T	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.874C>T	16.37:g.31200485C>T						FUS_ENST00000568685.1_Silent_p.L293L|FUS_ENST00000474990.1_3'UTR|FUS_ENST00000380244.3_Silent_p.L291L	p.L292L	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)	9	979	+		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)	292			RRM.		Q9H4A8	Silent	SNP	ENST00000254108.7	37	c.874C>T	CCDS10707.1																																																																																				0.388	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960		262	1088	0	0	0	1	0	262	1088				
SBF2	81846	broad.mit.edu	37	11	9853827	9853827	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:9853827C>T	ENST00000256190.8	-	27	3733	c.3596G>A	c.(3595-3597)gGa>gAa	p.G1199E		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1199	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CCCATGGAATCCTCCAGATCG	0.483																																						ENST00000256190.8																			0				breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						c.(3595-3597)gGa>gAa		SET binding factor 2							98.0	93.0	95.0					11																	9853827		2201	4294	6495	SO:0001583	missense	81846				myelination	cytoplasm|membrane	phosphatase activity|protein binding	g.chr11:9853827C>T	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3596G>A	11.37:g.9853827C>T	ENSP00000256190:p.Gly1199Glu						p.G1199E	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN		all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)	27	3733	-			1199			Myotubularin phosphatase.		Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	c.3596G>A	CCDS31427.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.181681|5.181681	0.94885|0.94885	.|.	.|.	ENSG00000133812|ENSG00000133812	ENST00000530741|ENST00000256190	.|D	.|0.92545	.|-3.06	5.76|5.76	5.76|5.76	0.90799|0.90799	.|Myotubularin phosphatase domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95787|0.95787	0.8629|0.8629	M|M	0.66506|0.66506	2.035|2.035	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.81914	.|0.995	D|D	0.95369|0.95369	0.8462|0.8462	5|10	.|0.66056	.|D	.|0.02	.|.	20.3242|20.3242	0.98691|0.98691	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1199	.|Q86WG5	.|MTMRD_HUMAN	N|E	83|1199	.|ENSP00000256190:G1199E	.|ENSP00000256190:G1199E	D|G	-|-	1|2	0|0	SBF2|SBF2	9810403|9810403	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.764000|7.764000	0.85297|0.85297	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GAT|GGA		0.483	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		75	226	0	0	0	1	0	75	226				
DAB2	1601	broad.mit.edu	37	5	39383071	39383071	+	Silent	SNP	C	C	T	rs199558080		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:39383071C>T	ENST00000320816.6	-	10	1457	c.990G>A	c.(988-990)ccG>ccA	p.P330P	DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000509337.1_Silent_p.P309P|DAB2_ENST00000545653.1_Silent_p.P309P|DAB2_ENST00000339788.6_Intron	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	330	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			CATTACTCAGCGGAGTAGACG	0.483													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19568	0.0		0.0	False		,,,				2504	0.0					ENST00000545653.1																			0				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47						c.(925-927)ccG>ccA		Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)		C		1,4405	2.1+/-5.4	0,1,2202	94.0	98.0	96.0		990	-4.7	1.0	5		96	0,8600		0,0,4300	no	coding-synonymous	DAB2	NM_001343.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		330/771	39383071	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1601				cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding	g.chr5:39383071C>T	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.990G>A	5.37:g.39383071C>T						DAB2_ENST00000509337.1_Silent_p.P309P|DAB2_ENST00000339788.6_Intron|DAB2_ENST00000320816.6_Silent_p.P330P	p.P309P	NM_001244871.1	NP_001231800.1	P98082	DAB2_HUMAN	Epithelial(62;0.137)		9	1457	-	all_lung(31;0.000197)		330					A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	c.927G>A	CCDS34149.1																																																																																				0.483	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		97	485	0	0	0	1	0	97	485				
GPR98	84059	broad.mit.edu	37	5	89971103	89971103	+	Silent	SNP	C	C	T	rs371138490		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:89971103C>T	ENST00000405460.2	+	24	5250	c.5154C>T	c.(5152-5154)gaC>gaT	p.D1718D	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1718	Calx-beta 12. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGCCTAAGGACGCAATGACCC	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16840	0.0		0.0	False		,,,				2504	0.0					ENST00000405460.2																			0				NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269						c.(5152-5154)gaC>gaT		G protein-coupled receptor 98		C		4,4166		0,4,2081	62.0	65.0	64.0		5154	-4.0	0.0	5		64	0,8434		0,0,4217	no	coding-synonymous	GPR98	NM_032119.3		0,4,6298	TT,TC,CC		0.0,0.0959,0.0317		1718/6307	89971103	4,12600	2085	4217	6302	SO:0001819	synonymous_variant	84059				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr5:89971103C>T	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5154C>T	5.37:g.89971103C>T						GPR98_ENST00000450321.2_3'UTR	p.D1718D	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	24	5250	+		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)	1718					O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	c.5154C>T	CCDS47246.1																																																																																				0.527	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		22	173	0	0	0	1	0	22	173				
BMS1P20	96610	broad.mit.edu	37	22	22661187	22661187	+	RNA	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:22661187G>A	ENST00000426066.1	+	0	279					NR_027293.1				BMS1 pseudogene 20																		CCCCCACCCCGTCATGTACAG	0.413																																						ENST00000426066.1																			0																																																			0							g.chr22:22661187G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661187G>A								NR_027293.1						0	279	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.413	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			18	147	0	0	0	1	0	18	147				
RRN3P2	653390	broad.mit.edu	37	16	29110458	29110458	+	RNA	SNP	T	T	C	rs561841139		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:29110458T>C	ENST00000564580.1	+	0	1131							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2									p.W375R(25)									GAATTTTGAGTGGATAGTGAT	0.328																																						ENST00000564580.1																			25	Substitution - Missense(25)	p.W375R(25)	endometrium(19)|kidney(4)|prostate(2)																																																0							g.chr16:29110458T>C			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29110458T>C														0	1131	+									RNA	SNP	ENST00000564580.1	37			.	.	.	.	.	.	.	.	.	.	N	5.632	0.301362	0.10678	.	.	ENSG00000103472	ENST00000427965	.	.	.	1.93	1.93	0.25924	.	0.000000	0.64402	N	0.000001	T	0.11239	0.0274	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29701	-1.0003	5	0.02654	T	1	.	2.7527	0.05285	0.2724:0.5536:0.0:0.174	.	.	.	.	R	375	.	ENSP00000398611:W375R	W	+	1	0	AC009093.1	29017959	1.000000	0.71417	0.564000	0.28396	0.423000	0.31445	3.439000	0.52878	0.163000	0.19507	-1.160000	0.01791	TGG		0.328	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433243.1	NR_003369		28	286	0	0	0	1	0	28	286				
ESPNP	284729	broad.mit.edu	37	1	17046595	17046595	+	RNA	SNP	T	T	C	rs3856293	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:17046595T>C	ENST00000492551.1	-	0	57					NR_026567.1				espin pseudogene																		TTCACCACCTTGGGGTGGCCA	0.592																																						ENST00000492551.1																			0																																																			0							g.chr1:17046595T>C	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17046595T>C								NR_026567.1						0	57	-									RNA	SNP	ENST00000492551.1	37																																																																																						0.592	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			14	324	0	0	0	1	0	14	324				
LYZL4	131375	broad.mit.edu	37	3	42448399	42448399	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:42448399C>A	ENST00000287748.3	-	3	506	c.231G>T	c.(229-231)caG>caT	p.Q77H	LYZL4_ENST00000470991.1_5'UTR|LYZL4_ENST00000441172.1_Missense_Mutation_p.Q77H	NM_144634.2	NP_653235.1	Q96KX0	LYZL4_HUMAN	lysozyme-like 4	77					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)|nucleus (GO:0005634)	lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(1)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TGCCACGCATCTGAAAGAGGC	0.577																																						ENST00000287748.3																			0				central_nervous_system(1)|endometrium(1)|lung(1)	3						c.(229-231)caG>caT		lysozyme-like 4							98.0	83.0	88.0					3																	42448399		2203	4300	6503	SO:0001583	missense	131375				cell wall macromolecule catabolic process	extracellular region	lysozyme activity	g.chr3:42448399C>A	BC016747, AF326749	CCDS2697.1	3p21.33	2006-04-12			ENSG00000157093	ENSG00000157093			28387	protein-coding gene	gene with protein product		612750				12477932	Standard	NM_144634		Approved	MGC26768, LYC4	uc003cle.3	Q96KX0	OTTHUMG00000131793	ENST00000287748.3:c.231G>T	3.37:g.42448399C>A	ENSP00000287748:p.Gln77His					LYZL4_ENST00000470991.1_5'UTR|LYZL4_ENST00000441172.1_Missense_Mutation_p.Q77H	p.Q77H	NM_144634.2	NP_653235.1	Q96KX0	LYZL4_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.222)	3	506	-			77						Missense_Mutation	SNP	ENST00000287748.3	37	c.231G>T	CCDS2697.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.334712	0.41297	.	.	ENSG00000157093	ENST00000287748;ENST00000441172	T;T	0.78481	-1.18;-1.18	4.31	3.42	0.39159	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000002	D	0.89543	0.6745	H	0.95780	3.72	0.37506	D	0.916944	D	0.89917	1.0	D	0.91635	0.999	D	0.91121	0.4930	10	0.87932	D	0	-19.1719	7.4537	0.27252	0.0:0.8802:0.0:0.1198	.	77	Q96KX0	LYZL4_HUMAN	H	77	ENSP00000287748:Q77H;ENSP00000387897:Q77H	ENSP00000287748:Q77H	Q	-	3	2	LYZL4	42423403	1.000000	0.71417	0.999000	0.59377	0.253000	0.25986	1.310000	0.33551	2.105000	0.64084	0.563000	0.77884	CAG		0.577	LYZL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254729.2	NM_144634		70	224	1	0	2.72615e-36	1	3.00183e-36	70	224				
ZNF99	7652	broad.mit.edu	37	19	22940448	22940448	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:22940448G>T	ENST00000596209.1	-	4	2353	c.2263C>A	c.(2263-2265)Cat>Aat	p.H755N	ZNF99_ENST00000397104.3_Missense_Mutation_p.H664N|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	755					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H664D(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TCTGCAGTATGAATTACCTTA	0.353																																						ENST00000397104.3																			1	Substitution - Missense(1)	p.H664D(1)	lung(1)	NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124						c.(1990-1992)Cat>Aat		zinc finger protein 99							26.0	27.0	27.0					19																	22940448		1904	4049	5953	SO:0001583	missense	7652							g.chr19:22940448G>T	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2263C>A	19.37:g.22940448G>T	ENSP00000472969:p.His755Asn					ZNF99_ENST00000596209.1_Missense_Mutation_p.H755N	p.H664N							5	1989	-		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)						M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	c.1990C>A	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	g	12.79	2.043291	0.36085	.	.	ENSG00000213973	ENST00000397104	T	0.28895	1.59	0.726	0.726	0.18248	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.62109	0.2401	H	0.94542	3.55	0.24997	N	0.991498	D	0.89917	1.0	D	0.97110	1.0	T	0.50608	-0.8808	9	0.87932	D	0	.	8.9692	0.35897	0.0:0.0:1.0:0.0	.	664	A8MXY4	ZNF99_HUMAN	N	664	ENSP00000380293:H664N	ENSP00000380293:H664N	H	-	1	0	ZNF99	22732288	0.998000	0.40836	0.006000	0.13384	0.035000	0.12851	4.228000	0.58619	0.680000	0.31366	0.400000	0.26472	CAT		0.353	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		47	264	1	0	1.56989e-16	1	1.67228e-16	47	264				
BCL11B	64919	broad.mit.edu	37	14	99640770	99640770	+	Silent	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:99640770G>A	ENST00000357195.3	-	4	2412	c.2403C>T	c.(2401-2403)tgC>tgT	p.C801C	BCL11B_ENST00000345514.2_Silent_p.C730C|BCL11B_ENST00000443726.2_Silent_p.C607C	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	801					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		ACACCTTGCCGCAGTACTCGC	0.721			T	TLX3	T-ALL																																	ENST00000345514.2				Dom	yes		14	14q32.1	64919	T	B-cell CLL/lymphoma 11B  (CTIP2)			L	TLX3		T-ALL		0				NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34						c.(2188-2190)tgC>tgT		B-cell CLL/lymphoma 11B (zinc finger protein)							30.0	26.0	27.0					14																	99640770		2202	4298	6500	SO:0001819	synonymous_variant	64919					nucleus	zinc ion binding	g.chr14:99640770G>A	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"""Zinc fingers, C2H2-type"""	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2403C>T	14.37:g.99640770G>A						BCL11B_ENST00000357195.3_Silent_p.C801C|BCL11B_ENST00000443726.2_Silent_p.C607C	p.C730C	NM_022898.1	NP_075049.1	Q9C0K0	BC11B_HUMAN		COAD - Colon adenocarcinoma(157;0.103)	3	2456	-		Melanoma(154;0.0866)|all_epithelial(191;0.241)	801					Q9H162	Silent	SNP	ENST00000357195.3	37	c.2190C>T	CCDS9950.1																																																																																				0.721	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		27	103	0	0	0	1	0	27	103				
CNTD2	79935	broad.mit.edu	37	19	40729348	40729348	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:40729348C>A	ENST00000430325.2	-	4	667	c.619G>T	c.(619-621)Ggc>Tgc	p.G207C	CNTD2_ENST00000513948.1_Missense_Mutation_p.G101C	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	207					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						AGCAGCGGGCCGGGGTGGTGC	0.726																																						ENST00000430325.2																			0				lung(1)|prostate(1)	2						c.(619-621)Ggc>Tgc		cyclin N-terminal domain containing 2							5.0	9.0	8.0					19																	40729348		671	1554	2225	SO:0001583	missense	79935				regulation of cyclin-dependent protein kinase activity		protein kinase binding	g.chr19:40729348C>A	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.619G>T	19.37:g.40729348C>A	ENSP00000396755:p.Gly207Cys					CNTD2_ENST00000513948.1_Missense_Mutation_p.G101C	p.G207C	NM_024877.3	NP_079153.2	B4DX65	B4DX65_HUMAN			4	667	-			207					B4DX65	Missense_Mutation	SNP	ENST00000430325.2	37	c.619G>T	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	C	12.98	2.101787	0.37048	.	.	ENSG00000105219	ENST00000430325;ENST00000513948	T;T	0.30981	1.51;1.52	4.02	4.02	0.46733	.	.	.	.	.	T	0.40570	0.1122	N	0.24115	0.695	0.26488	N	0.974985	D	0.89917	1.0	D	0.75020	0.985	T	0.22452	-1.0216	9	0.54805	T	0.06	.	13.1598	0.59538	0.0:1.0:0.0:0.0	.	207	B4DX65	.	C	207;101	ENSP00000396755:G207C;ENSP00000425529:G101C	ENSP00000396755:G207C	G	-	1	0	CNTD2	45421188	0.020000	0.18652	0.109000	0.21407	0.116000	0.19942	1.586000	0.36611	2.078000	0.62432	0.561000	0.74099	GGC		0.726	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877		31	90	1	0	6.38683e-12	1	6.73021e-12	31	90				
SUGT1	10910	broad.mit.edu	37	13	53254258	53254258	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr13:53254258G>C	ENST00000343788.6	+	13	1046	c.964G>C	c.(964-966)Gat>Cat	p.D322H	SUGT1_ENST00000310528.8_Missense_Mutation_p.D290H|SUGT1_ENST00000535397.1_Missense_Mutation_p.D234H	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	322	SGS. {ECO:0000255|PROSITE- ProRule:PRU00386}.				innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		AGATGGTTCTGATGAAGTGAA	0.313																																						ENST00000535397.1																			0				kidney(3)|large_intestine(3)|lung(2)	8						c.(700-702)Gat>Cat		SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)							98.0	105.0	103.0					13																	53254258		2203	4300	6503	SO:0001583	missense	10910				mitosis	kinetochore|ubiquitin ligase complex	binding	g.chr13:53254258G>C	AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.964G>C	13.37:g.53254258G>C	ENSP00000367208:p.Asp322His					SUGT1_ENST00000343788.6_Missense_Mutation_p.D322H|SUGT1_ENST00000310528.7_Missense_Mutation_p.D290H	p.D234H			Q9Y2Z0	SUGT1_HUMAN		GBM - Glioblastoma multiforme(99;3.25e-08)	13	1073	+		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)	322			CS.		A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Missense_Mutation	SNP	ENST00000343788.6	37	c.700G>C	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903552	0.72754	.	.	ENSG00000165416	ENST00000343788;ENST00000535397;ENST00000310528	T;T	0.31769	1.48;1.53	5.22	4.38	0.52667	SGS (2);HSP20-like chaperone (1);	0.000000	0.85682	D	0.000000	T	0.63141	0.2486	M	0.91196	3.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.999;0.998	T	0.72818	-0.4178	10	0.72032	D	0.01	-21.0837	14.094	0.65008	0.0731:0.0:0.9269:0.0	.	234;234;322;290	F5H5A9;B4DYC6;Q9Y2Z0;Q9Y2Z0-2	.;.;SUGT1_HUMAN;.	H	322;234;290	ENSP00000367208:D322H;ENSP00000308067:D290H	ENSP00000308067:D290H	D	+	1	0	SUGT1	52152259	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.420000	0.97426	1.329000	0.45376	0.467000	0.42956	GAT		0.313	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2			260	252	0	0	0	1	0	260	252				
PDE10A	10846	broad.mit.edu	37	6	165809905	165809905	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:165809905G>A	ENST00000366882.1	-	15	1446	c.1292C>T	c.(1291-1293)aCg>aTg	p.T431M	PDE10A_ENST00000539869.2_Missense_Mutation_p.T441M|PDE10A_ENST00000354448.4_Missense_Mutation_p.T431M			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	431					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.T431M(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	CTTTTCCATCGTTACCCGGTA	0.393																																					Esophageal Squamous(22;308 615 5753 12038 40624)	ENST00000366882.1																			1	Substitution - Missense(1)	p.T431M(1)	large_intestine(1)	breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71						c.(1291-1293)aCg>aTg		phosphodiesterase 10A	Dipyridamole(DB00975)						190.0	159.0	170.0					6																	165809905		2203	4300	6503	SO:0001583	missense	10846				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding	g.chr6:165809905G>A	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.1292C>T	6.37:g.165809905G>A	ENSP00000355847:p.Thr431Met					PDE10A_ENST00000539869.2_Missense_Mutation_p.T441M|PDE10A_ENST00000354448.4_Missense_Mutation_p.T431M	p.T431M			Q9Y233	PDE10_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	15	1446	-		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)	431					Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37	c.1292C>T		.	.	.	.	.	.	.	.	.	.	G	22.0	4.233162	0.79688	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69806	-0.43;-0.43	5.34	5.34	0.76211	.	1.162770	0.06098	N	0.664795	T	0.79981	0.4540	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.80764	0.994;0.882	T	0.71823	-0.4476	10	0.52906	T	0.07	.	19.0469	0.93025	0.0:0.0:1.0:0.0	.	441;431	Q9ULW9;Q9Y233	.;PDE10_HUMAN	M	431;459;441;431;430	ENSP00000355847:T431M;ENSP00000346435:T431M	ENSP00000341187:T441M	T	-	2	0	PDE10A	165729895	1.000000	0.71417	0.148000	0.22405	0.607000	0.37147	9.409000	0.97331	2.508000	0.84585	0.650000	0.86243	ACG		0.393	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			165	436	0	0	0	1	0	165	436				
ZMIZ2	83637	broad.mit.edu	37	7	44801069	44801069	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:44801069T>G	ENST00000309315.4	+	10	1385	c.1262T>G	c.(1261-1263)tTg>tGg	p.L421W	ZMIZ2_ENST00000441627.1_Missense_Mutation_p.L421W|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.L363W|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.L389W|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.L395W	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	421					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TGTGACGAGTTGCGGCTGACC	0.637																																					NSCLC(20;604 852 1948 16908 50522)	ENST00000309315.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(1261-1263)tTg>tGg		zinc finger, MIZ-type containing 2							48.0	58.0	55.0					7																	44801069		2202	4299	6501	SO:0001583	missense	83637				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding	g.chr7:44801069T>G	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.1262T>G	7.37:g.44801069T>G	ENSP00000311778:p.Leu421Trp					ZMIZ2_ENST00000441627.1_Missense_Mutation_p.L421W|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.L389W|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.L363W|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.L395W	p.L421W	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN			10	1385	+			421					A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	c.1262T>G	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.744049	0.89663	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	4.91	4.91	0.64330	.	0.000000	0.46145	D	0.000305	T	0.66436	0.2789	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.70245	-0.4925	10	0.72032	D	0.01	-8.1827	14.3763	0.66879	0.0:0.0:0.0:1.0	.	395;421;363	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	W	363;421;421;389;395;421	ENSP00000409648:L363W;ENSP00000311778:L421W;ENSP00000414723:L421W;ENSP00000396601:L389W;ENSP00000265346:L395W	ENSP00000265346:L395W	L	+	2	0	ZMIZ2	44767594	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	7.408000	0.80041	2.060000	0.61445	0.533000	0.62120	TTG		0.637	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		56	280	0	0	0	1	0	56	280				
CDK14	5218	broad.mit.edu	37	7	90356126	90356126	+	Splice_Site	SNP	G	G	C	rs55722725		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:90356126G>C	ENST00000380050.3	+	3	500	c.369G>C	c.(367-369)tcG>tcC	p.S123S	CDK14_ENST00000436577.2_Splice_Site_p.R26P|CDK14_ENST00000265741.3_Splice_Site_p.S105S|CDK14_ENST00000406263.1_Splice_Site_p.S77S			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	123					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						GCCCCAGCTCGGTAAGTGCAG	0.463																																					GBM(83;1228 1256 8311 16577 31299)	ENST00000406263.1																			0				breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						c.e2+1		cyclin-dependent kinase 14							64.0	61.0	62.0					7																	90356126		2203	4299	6502	SO:0001630	splice_region_variant	5218				cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity	g.chr7:90356126G>C		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"""Cyclin-dependent kinases"""	8883	protein-coding gene	gene with protein product		610679	"""PFTAIRE protein kinase 1"""	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.369+1G>C	7.37:g.90356126G>C						CDK14_ENST00000380050.3_Splice_Site_p.S123_splice|CDK14_ENST00000436577.2_Splice_Site_p.R26_splice|CDK14_ENST00000265741.3_Splice_Site_p.S105_splice	p.S77_splice			O94921	CDK14_HUMAN			2	673	+			123					A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Splice_Site	SNP	ENST00000380050.3	37	c.231_splice		.	.	.	.	.	.	.	.	.	.	G	14.74	2.624665	0.46840	.	.	ENSG00000058091	ENST00000436577	T	0.46451	0.87	5.51	4.6	0.57074	.	.	.	.	.	T	0.38585	0.1046	.	.	.	0.19775	N	0.999956	P	0.43287	0.802	B	0.39465	0.3	T	0.38415	-0.9662	8	0.87932	D	0	-2.8377	14.3863	0.66947	0.0:0.0:0.7431:0.2569	.	26	E7EUK8	.	P	26	ENSP00000398936:R26P	ENSP00000398936:R26P	R	+	2	0	CDK14	90194062	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.836000	0.39191	2.588000	0.87417	0.563000	0.77884	CGG		0.463	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395	Silent	199	306	0	0	0	1	0	199	306				
LMX1B	4010	broad.mit.edu	37	9	129455511	129455511	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:129455511G>A	ENST00000373474.4	+	4	657	c.650G>A	c.(649-651)cGg>cAg	p.R217Q	LMX1B_ENST00000425646.2_Missense_Mutation_p.R194Q|LMX1B_ENST00000355497.5_Missense_Mutation_p.R217Q|LMX1B_ENST00000526117.1_Missense_Mutation_p.R217Q|LMX1B_ENST00000561065.1_Missense_Mutation_p.R194Q			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	217					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						AAGGACCCGCGGAGGCCCAAG	0.652									Nail-Patella Syndrome																												Pancreas(110;1796 2278 18357 20466)	ENST00000355497.5																			0				endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						c.(649-651)cGg>cAg		LIM homeobox transcription factor 1, beta							37.0	39.0	39.0					9																	129455511		2202	4300	6502	SO:0001583	missense	4010	Nail-Patella Syndrome	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	dorsal/ventral pattern formation|in utero embryonic development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr9:129455511G>A	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"""Homeoboxes / LIM class"""	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.650G>A	9.37:g.129455511G>A	ENSP00000362573:p.Arg217Gln					LMX1B_ENST00000373474.4_Missense_Mutation_p.R217Q|LMX1B_ENST00000425646.2_Missense_Mutation_p.R194Q|LMX1B_ENST00000526117.1_Missense_Mutation_p.R217Q|LMX1B_ENST00000561065.1_Missense_Mutation_p.R194Q	p.R217Q	NM_001174146.1	NP_001167617.1	O60663	LMX1B_HUMAN			4	657	+			194					F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	37	c.650G>A	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989886	0.93106	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497;ENST00000425646	T;T;D;T	0.95853	-1.08;-1.08;-3.83;-1.08	4.97	4.97	0.65823	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.93180	0.7828	L	0.51422	1.61	0.80722	D	1	P;P;D	0.55800	0.8;0.88;0.973	B;B;B	0.44108	0.206;0.164;0.441	D	0.91782	0.5436	10	0.10636	T	0.68	.	17.2153	0.86941	0.0:0.0:1.0:0.0	.	194;194;217	B7ZLH2;O60663;F8VYP0	.;LMX1B_HUMAN;.	Q	217;217;217;194	ENSP00000436930:R217Q;ENSP00000362573:R217Q;ENSP00000347684:R217Q;ENSP00000390923:R194Q	ENSP00000347684:R217Q	R	+	2	0	LMX1B	128495332	1.000000	0.71417	0.882000	0.34594	0.936000	0.57629	6.381000	0.73163	2.299000	0.77371	0.462000	0.41574	CGG		0.652	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			7	81	0	0	0	1	0	7	81				
SIRPB1	10326	broad.mit.edu	37	20	1585397	1585397	+	Intron	SNP	T	T	C	rs148754551	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr20:1585397T>C	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381596.1_5'Flank|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|SIRPB1_ENST00000279477.7_Missense_Mutation_p.T248A|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381603.3_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.T248A(5)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTCGGATGGTCTCAGACAAG	0.627													t|||	2569	0.512979	0.6967	0.33	5008	,	,		3683	0.4435		0.4473	False		,,,				2504	0.5337					ENST00000279477.7																			5	Substitution - Missense(5)	p.T248A(5)	kidney(3)|prostate(2)	central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						c.(742-744)Acc>Gcc		signal-regulatory protein beta 1							20.0	30.0	27.0					20																	1585397		375	895	1270	SO:0001627	intron_variant	10326				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding	g.chr20:1585397T>C	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+15117A>G	20.37:g.1585397T>C						SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|SIRPB1_ENST00000381605.4_Intron	p.T248A	NM_001135844.2	NP_001129316.1	O00241	SIRB1_HUMAN			3	806	-			248					A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	c.742A>G	CCDS13019.1	757	0.3466117216117216	239	0.48577235772357724	97	0.26795580110497236	219	0.38286713286713286	202	0.26649076517150394	.	0.464	-0.887787	0.02511	.	.	ENSG00000101307	ENST00000279477	T	0.11930	2.73	2.24	-0.597	0.11653	.	.	.	.	.	T	0.00012	0.0000	N	0.20530	0.585	0.47778	P	4.809999999999537E-4	B	0.02656	0.0	B	0.06405	0.002	T	0.45483	-0.9258	8	0.13470	T	0.59	.	3.263	0.06855	0.2055:0.1485:0.0:0.646	.	248	Q5TFQ8	SIRBL_HUMAN	A	248	ENSP00000279477:T248A	ENSP00000279477:T248A	T	-	1	0	SIRPB1	1533397	0.001000	0.12720	0.631000	0.29282	0.161000	0.22273	-0.285000	0.08410	-0.814000	0.04352	-1.120000	0.02017	ACC		0.627	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		22	232	0	0	0	1	0	22	232				
CWH43	80157	broad.mit.edu	37	4	49019292	49019292	+	Silent	SNP	T	T	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:49019292T>C	ENST00000226432.4	+	9	1396	c.1213T>C	c.(1213-1215)Ttg>Ctg	p.L405L	CWH43_ENST00000513409.1_Silent_p.L378L	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	405					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						TGGTGTGGGATTGTTGGGATT	0.308																																						ENST00000226432.4																			0				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						c.(1213-1215)Ttg>Ctg		cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)							99.0	101.0	100.0					4																	49019292		2203	4300	6503	SO:0001819	synonymous_variant	80157				GPI anchor biosynthetic process	integral to membrane		g.chr4:49019292T>C		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1213T>C	4.37:g.49019292T>C						CWH43_ENST00000513409.1_Silent_p.L378L	p.L405L	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN			9	1396	+			405					B2RPD7	Silent	SNP	ENST00000226432.4	37	c.1213T>C	CCDS3486.1																																																																																				0.308	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		78	219	0	0	0	1	0	78	219				
ARMCX1	51309	broad.mit.edu	37	X	100808322	100808322	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:100808322A>G	ENST00000372829.3	+	4	780	c.409A>G	c.(409-411)Acc>Gcc	p.T137A		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	137						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						TGGGAACAGGACCCTTGCACC	0.612																																						ENST00000372829.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						c.(409-411)Acc>Gcc		armadillo repeat containing, X-linked 1							74.0	68.0	70.0					X																	100808322		2203	4300	6503	SO:0001583	missense	51309					integral to membrane	binding	g.chrX:100808322A>G	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"""Armadillo repeat containing"""	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.409A>G	X.37:g.100808322A>G	ENSP00000361917:p.Thr137Ala						p.T137A	NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN			4	780	+			137					Q53HK2|Q9H2Q0	Missense_Mutation	SNP	ENST00000372829.3	37	c.409A>G	CCDS14487.1	.	.	.	.	.	.	.	.	.	.	a	9.041	0.989764	0.18966	.	.	ENSG00000126947	ENST00000372829	T	0.28454	1.61	3.86	1.39	0.22231	.	0.509670	0.16809	N	0.198655	T	0.11153	0.0272	N	0.12182	0.205	0.24652	N	0.993514	B	0.06786	0.001	B	0.04013	0.001	T	0.33523	-0.9865	10	0.02654	T	1	-1.2837	3.4353	0.07444	0.6406:0.2323:0.1271:0.0	.	137	Q9P291	ARMX1_HUMAN	A	137	ENSP00000361917:T137A	ENSP00000361917:T137A	T	+	1	0	ARMCX1	100694978	0.868000	0.29978	0.977000	0.42913	0.890000	0.51754	0.859000	0.27858	0.166000	0.19597	0.451000	0.29950	ACC		0.612	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		101	262	0	0	0	1	0	101	262				
CDKN2A	1029	broad.mit.edu	37	9	21971120	21971120	+	Nonsense_Mutation	SNP	G	G	A	rs121913388		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:21971120G>A	ENST00000304494.5	-	2	508	c.238C>T	c.(238-240)Cga>Tga	p.R80*	CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	80			R -> L (in a head and neck tumor).|R -> P (in CMM2; loss of CDK4 binding). {ECO:0000269|PubMed:19260062}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TGCACGGGTCGGGTGAGAGTG	0.726	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																												ENST00000304494.5	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17																	1474	Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1)	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)	haematopoietic_and_lymphoid_tissue(298)|skin(206)|central_nervous_system(168)|lung(150)|urinary_tract(91)|bone(76)|oesophagus(72)|upper_aerodigestive_tract(63)|soft_tissue(60)|pleura(51)|pancreas(37)|ovary(36)|kidney(32)|breast(32)|biliary_tract(16)|thyroid(15)|NS(14)|stomach(14)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(3)|endometrium(3)|prostate(2)	NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199	GRCh37	CM014695	CDKN2A	M	rs121913388	c.(238-240)Cga>Tga		cyclin-dependent kinase inhibitor 2A							11.0	14.0	13.0					9																	21971120		2172	4246	6418	SO:0001587	stop_gained	1029				cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein kinase binding	g.chr9:21971120G>A	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.238C>T	9.37:g.21971120G>A	ENSP00000307101:p.Arg80*	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)				CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*	p.R80*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	2	508	-		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)	80		R -> L (in a head and neck tumor).|R -> P (in CMM2; loss of CDK4 binding).			A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	37	c.238C>T	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.328457|7.328457	0.98214|0.98214	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	D;D|.	0.86497|.	-2.13;-2.02|.	5.93|5.93	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.37136|.	N|.	0.002233|.	T|.	0.44561|.	0.1299|.	L|L	0.36672|0.36672	1.1|1.1	0.47511|0.47511	D|D	0.999443|0.999443	D|.	0.59357|.	0.985|.	B|.	0.40602|.	0.334|.	T|.	0.34825|.	-0.9813|.	10|.	0.13108|0.02654	T|T	0.6|1	-2.989|-2.989	8.7197|8.7197	0.34434|0.34434	0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526	.|.	135|.	Q8N726|.	CD2A2_HUMAN|.	L|X	135;94|80	ENSP00000355153:P135L;ENSP00000432664:P94L|.	ENSP00000355153:P135L|ENSP00000307101:R80X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961120|21961120	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	2.363000|2.363000	0.44178|0.44178	1.464000|1.464000	0.47987|0.47987	0.650000|0.650000	0.86243|0.86243	CCG|CGA		0.726	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		38	50	0	0	0	1	0	38	50				
GPRC5B	51704	broad.mit.edu	37	16	19883256	19883256	+	Silent	SNP	C	C	T	rs199673129		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:19883256C>T	ENST00000300571.2	-	2	1103	c.912G>A	c.(910-912)acG>acA	p.T304T	GPRC5B_ENST00000569847.1_Silent_p.T304T|GPRC5B_ENST00000535671.1_Silent_p.T304T|GPRC5B_ENST00000537135.1_Silent_p.T330T|GPRC5B_ENST00000569479.1_Silent_p.T304T	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	304					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGTAGTTGGGCGTGTTCTCCT	0.637																																						ENST00000300571.2																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						c.(910-912)acG>acA		G protein-coupled receptor, family C, group 5, member B							83.0	77.0	79.0					16																	19883256		2197	4300	6497	SO:0001819	synonymous_variant	0							g.chr16:19883256C>T	AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.912G>A	16.37:g.19883256C>T						GPRC5B_ENST00000535671.1_Silent_p.T304T|GPRC5B_ENST00000537135.1_Silent_p.T330T|GPRC5B_ENST00000569479.1_Silent_p.T304T|GPRC5B_ENST00000569847.1_Silent_p.T304T	p.T304T	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN			2	1103	-			304					D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	c.912G>A	CCDS10581.1																																																																																				0.637	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			66	321	0	0	0	1	0	66	321				
ZNF675	171392	broad.mit.edu	37	19	23836431	23836431	+	Missense_Mutation	SNP	C	C	T	rs552345271		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:23836431C>T	ENST00000359788.4	-	4	1472	c.1304G>A	c.(1303-1305)cGa>cAa	p.R435Q	ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	435					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTTGAGGATCGGTTAAAAGC	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		19112	0.0		0.0	False		,,,				2504	0.001					ENST00000359788.4																			0				endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27						c.(1303-1305)cGa>cAa		zinc finger protein 675							51.0	55.0	54.0					19																	23836431		2202	4300	6502	SO:0001583	missense	171392				bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding	g.chr19:23836431C>T		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.1304G>A	19.37:g.23836431C>T	ENSP00000352836:p.Arg435Gln					ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron	p.R435Q	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN			4	1472	-		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)	435					Q8N211	Missense_Mutation	SNP	ENST00000359788.4	37	c.1304G>A	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	0.409	-0.914248	0.02415	.	.	ENSG00000197372	ENST00000359788	T	0.07444	3.19	0.876	-1.75	0.08031	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03263	0.0095	N	0.12443	0.215	0.09310	N	1	B	0.22909	0.077	B	0.12837	0.008	T	0.46624	-0.9178	9	0.08381	T	0.77	.	5.1337	0.14924	0.0:0.3802:0.0:0.6198	.	435	Q8TD23	ZN675_HUMAN	Q	435	ENSP00000352836:R435Q	ENSP00000352836:R435Q	R	-	2	0	ZNF675	23628271	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	-3.295000	0.00523	-0.722000	0.04922	-0.708000	0.03648	CGA		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		140	216	0	0	0	1	0	140	216				
CDH11	1009	broad.mit.edu	37	16	64984898	64984898	+	Missense_Mutation	SNP	G	G	A	rs147033764		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:64984898G>A	ENST00000268603.4	-	12	2281	c.1666C>T	c.(1666-1668)Cgg>Tgg	p.R556W	CDH11_ENST00000394156.3_Missense_Mutation_p.R556W|CDH11_ENST00000566827.1_Missense_Mutation_p.R430W	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	556	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCTCCACGCCGGGCGTACACG	0.592			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																												ENST00000394156.3				Dom	yes		16	16q22.1	1009	T	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""			M	USP6		aneurysmal bone cysts		0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88						c.(1666-1668)Cgg>Tgg		cadherin 11, type 2, OB-cadherin (osteoblast)							53.0	52.0	52.0					16																	64984898		2203	4300	6503	SO:0001583	missense	1009				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding	g.chr16:64984898G>A	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1666C>T	16.37:g.64984898G>A	ENSP00000268603:p.Arg556Trp	TSP Lung(24;0.17)				CDH11_ENST00000566827.1_Missense_Mutation_p.R430W|CDH11_ENST00000268603.4_Missense_Mutation_p.R556W	p.R556W			P55287	CAD11_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.205)	12	2119	-		Ovarian(137;0.0973)	556			Cadherin 5.		A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	c.1666C>T	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.319581	0.60524	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.61040	2.08;0.14	5.55	4.51	0.55191	Cadherin (3);Cadherin-like (1);	0.421596	0.26193	N	0.025782	T	0.72045	0.3412	M	0.89715	3.055	0.37759	D	0.926242	D;D	0.65815	0.995;0.991	P;P	0.53861	0.736;0.462	T	0.80058	-0.1541	10	0.87932	D	0	.	9.7974	0.40744	0.0:0.1189:0.6897:0.1914	.	556;556	P55287-2;P55287	.;CAD11_HUMAN	W	556;556;539	ENSP00000268603:R556W;ENSP00000377711:R556W	ENSP00000268603:R556W	R	-	1	2	CDH11	63542399	1.000000	0.71417	1.000000	0.80357	0.526000	0.34562	1.290000	0.33319	2.594000	0.87642	0.655000	0.94253	CGG		0.592	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		39	204	0	0	0	1	0	39	204				
MAST2	23139	broad.mit.edu	37	1	46494559	46494559	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:46494559delT	ENST00000361297.2	+	18	2455	c.2172delT	c.(2170-2172)cctfs	p.P724fs	MAST2_ENST00000372009.2_Frame_Shift_Del_p.P654fs	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GCTGCGTCCCTTTTTTTGGAG	0.552																																						ENST00000361297.2																			0				breast(1)|lung(3)|ovary(5)|stomach(2)	11						c.(2170-2172)ccfs		microtubule associated serine/threonine kinase 2							200.0	200.0	200.0					1																	46494559		1992	4175	6167	SO:0001589	frameshift_variant	23139				regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity	g.chr1:46494559delT	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.2172delT	1.37:g.46494559delT	ENSP00000354671:p.Pro724fs					MAST2_ENST00000372009.2_Frame_Shift_Del_p.P654fs|MAST2_ENST00000372008.1_Frame_Shift_Del_p.P609fs	p.P724fs	NM_015112.2	NP_055927.2	Q6P0Q8	MAST2_HUMAN			18	2455	+	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)		724			Protein kinase.			Frame_Shift_Del	DEL	ENST00000361297.2	37	c.2172delT	CCDS41326.1																																																																																				0.552	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		7	1135						7	1135	---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47325282	47325282	+	RNA	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:47325282delA	ENST00000505841.1	-	0	1204					NR_002788.2		Q8N1L4	CP4Z2_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 2, pseudogene							integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)										ATTTCAATCCAAACATAGCTG	0.393																																						ENST00000505841.1																			0																																																			0							g.chr1:47325282delA	AY262057		1p33	2013-07-25	2013-05-03		ENSG00000154198	ENSG00000154198		"""Cytochrome P450s"""	24426	pseudogene	pseudogene						15059886	Standard	NR_002788		Approved	FLJ40054	uc031pmm.1	Q8N1L4	OTTHUMG00000008024		1.37:g.47325282delA								NR_002788.2						0	1204	-								Q66ZJ5	RNA	DEL	ENST00000505841.1	37																																																																																						0.393	CYP4Z2P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361094.1	NR_002788		10	158						10	158	---	---	---	---
CCDC18	343099	broad.mit.edu	37	1	93667515	93667516	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:93667515_93667516insA	ENST00000343253.7	+	7	1267_1268	c.765_766insA	c.(766-768)aaafs	p.K256fs	CCDC18_ENST00000338949.4_Frame_Shift_Ins_p.K55fs|CCDC18_ENST00000557479.1_Frame_Shift_Ins_p.K374fs|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_Frame_Shift_Ins_p.K256fs			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	256								p.V377fs*15(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TCCAACAATATAAAAAAAAAGT	0.317																																						ENST00000343253.7																			1	Deletion - Frameshift(1)	p.V377fs*15(1)	ovary(1)	breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42						c.(763-768)taaaaafs		coiled-coil domain containing 18																																				SO:0001589	frameshift_variant	343099							g.chr1:93667515_93667516insA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.774dupA	1.37:g.93667524_93667524dupA	ENSP00000343377:p.Lys256fs					CCDC18_ENST00000338949.4_Frame_Shift_Ins_p.*K54fs|CCDC18_ENST00000401026.3_Frame_Shift_Ins_p.*K255fs|CCDC18_ENST00000557479.1_Frame_Shift_Ins_p.*K373fs|CCDC18_ENST00000334652.5_5'UTR	p.*K255fs			Q5T9S5	CCD18_HUMAN		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)	7	1267_1268	+		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)	255					Q6ZU17	Frame_Shift_Ins	INS	ENST00000343253.7	37	c.765_766insA																																																																																					0.317	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		11	214						11	214	---	---	---	---
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121137791	121137793	+	lincRNA	DEL	CCA	CCA	-	rs28552466|rs61625886|rs374710813	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:121137791_121137793delCCA	ENST00000417218.1	+	0	0				RP11-343N15.1_ENST00000437515.1_lincRNA																							ATTTCGCCCTCCACCGCCGCCGC	0.631																																						ENST00000437515.1																			0																																																			0							g.chr1:121137791_121137793delCCA																													1.37:g.121137791_121137793delCCA														0	329	-									RNA	DEL	ENST00000417218.1	37																																																																																						0.631	AL592494.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000036739.1			13	74						13	74	---	---	---	---
MCL1	4170	broad.mit.edu	37	1	150551492	150551494	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:150551492_150551494delTCC	ENST00000369026.2	-	1	572_574	c.513_515delGGA	c.(511-516)gaggac>gac	p.E171del	MCL1_ENST00000307940.3_In_Frame_Del_p.E171del|MCL1_ENST00000464132.1_5'Flank	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	171	PEST-like.				apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GTACAACTCGTCCTCCTCCTCCT	0.635																																						ENST00000369026.2																			0				endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8						c.(511-516)gac>ga		myeloid cell leukemia sequence 1 (BCL2-related)			,,	70,4190		29,12,2089					,,	1.0	1.0			54	109,8145		46,17,4064	no	coding,coding,intron	MCL1	NM_182763.2,NM_021960.4,NM_001197320.1	,,	75,29,6153	A1A1,A1R,RR		1.3206,1.6432,1.4304	,,	,,		179,12335				SO:0001651	inframe_deletion	4170				anti-apoptosis|apoptosis|cell fate determination|cellular homeostasis|multicellular organismal development|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nucleoplasm	BH3 domain binding|protein binding|protein channel activity|protein heterodimerization activity	g.chr1:150551492_150551494delTCC	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"""myeloid cell leukemia sequence 1 (BCL2-related)"""			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.513_515delGGA	1.37:g.150551501_150551503delTCC	ENSP00000358022:p.Glu171del					MCL1_ENST00000307940.3_In_Frame_Del_p.ED171del	p.ED171del	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		1	572_574	-	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		171			PEST-like.		B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	In_Frame_Del	DEL	ENST00000369026.2	37	c.513_515delGGA	CCDS957.1																																																																																				0.635	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		13	572						13	572	---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162326888	162326890	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:162326888_162326890delCAG	ENST00000361897.5	+	8	1303_1305	c.901_903delCAG	c.(901-903)cagdel	p.Q306del	NOS1AP_ENST00000530878.1_In_Frame_Del_p.Q301del	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	306	Poly-Gln.				regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			gcagctcctccagcagcAGCAGC	0.611																																						ENST00000361897.5																			0				NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32						c.(901-903)del		nitric oxide synthase 1 (neuronal) adaptor protein																																				SO:0001651	inframe_deletion	9722				regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding	g.chr1:162326888_162326890delCAG	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.901_903delCAG	1.37:g.162326897_162326899delCAG	ENSP00000355133:p.Gln306del					NOS1AP_ENST00000530878.1_In_Frame_Del_p.Q301del	p.Q306del	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.0537)		8	1303_1305	+	all_hematologic(112;0.203)		306			Poly-Gln.		B7ZLF5|O43564|Q3T551|Q5VU95	In_Frame_Del	DEL	ENST00000361897.5	37	c.901_903delCAG	CCDS1237.1																																																																																				0.611	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		8	442						8	442	---	---	---	---
SCYL3	57147	broad.mit.edu	37	1	169833511	169833511	+	Splice_Site	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:169833511delT	ENST00000367770.1	-	8	1001	c.954delA	c.(952-954)aaa>aa	p.K318fs	SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367772.4_Splice_Site_p.K318fs|SCYL3_ENST00000367771.6_Splice_Site_p.K318fs			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	318					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGCATTCACCTTTTTTGGGGC	0.393																																						ENST00000367772.4																			0				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						c.e9+1		SCY1-like 3 (S. cerevisiae)							92.0	94.0	94.0					1																	169833511		2203	4300	6503	SO:0001630	splice_region_variant	57147				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity	g.chr1:169833511delT	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"""ezrin-binding partner PACE-1"""	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.955+1A>-	1.37:g.169833511delT						SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367771.5_Splice_Site_p.K318_splice|SCYL3_ENST00000367770.1_Splice_Site_p.K318_splice	p.K318_splice	NM_181093.3	NP_851607.2	Q8IZE3	PACE1_HUMAN			9	1151	-	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)		318					A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Splice_Site	DEL	ENST00000367770.1	37	c.955_splice	CCDS1287.1																																																																																				0.393	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093	Frame_Shift_Del	7	737						7	737	---	---	---	---
GPR37L1	9283	broad.mit.edu	37	1	202097525	202097527	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr1:202097525_202097527delCTG	ENST00000367282.5	+	2	1393_1395	c.1287_1289delCTG	c.(1285-1290)gactgc>gac	p.C436del		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	436	Cys-rich.				negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						CCTTCCTGGActgctgctgctgc	0.626																																						ENST00000367282.4																			0				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						c.(1285-1290)gac>ga		G protein-coupled receptor 37 like 1				2,128,4136		0,0,2,9,110,2012						3.1	1.0			46	5,240,8007		0,0,5,10,220,3891	no	codingComplex	GPR37L1	NM_004767.3		0,0,7,19,330,5903	A1A1,A1A2,A1R,A2A2,A2R,RR		2.969,3.0474,2.9957				7,368,12143				SO:0001651	inframe_deletion	9283					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding	g.chr1:202097525_202097527delCTG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1287_1289delCTG	1.37:g.202097534_202097536delCTG	ENSP00000356251:p.Cys436del						p.DC429del	NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN			2	1393_1395	+			429			Cys-rich.		B2R7M9|Q5SXP7|Q86VP7	In_Frame_Del	DEL	ENST00000367282.5	37	c.1287_1289delCTG	CCDS1420.1																																																																																				0.626	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		8	204						8	204	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26022304	26022306	+	In_Frame_Del	DEL	CTG	CTG	-	rs539079430		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:26022304_26022306delCTG	ENST00000435504.4	-	5	644_646	c.351_353delCAG	c.(349-354)agcagt>agt	p.117_118SS>S	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000336112.4_In_Frame_Del_p.89_90SS>S|ASXL2_ENST00000497092.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	117	Ser-rich.				adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCACCATCACTGCTGCTGCTGC	0.463																																						ENST00000435504.4																			0				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33						c.(349-354)agt>ag		additional sex combs like 2 (Drosophila)																																				SO:0001651	inframe_deletion	55252				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding	g.chr2:26022304_26022306delCTG			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.351_353delCAG	2.37:g.26022313_26022315delCTG	ENSP00000391447:p.Ser118del					ASXL2_ENST00000336112.4_In_Frame_Del_p.SS89del|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR	p.SS117del			Q76L83	ASXL2_HUMAN			5	644_646	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		117			Ser-rich.		Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	In_Frame_Del	DEL	ENST00000435504.4	37	c.351_353delCAG																																																																																					0.463	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		10	917						10	917	---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29295647	29295649	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:29295647_29295649delTCC	ENST00000331664.5	-	1	1478_1480	c.1479_1481delGGA	c.(1477-1482)gaggaa>gaa	p.493_494EE>E		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	493					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CATTTTGTCTTCCTCCTCCTCCT	0.542																																						ENST00000331664.5																			0				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						c.(1477-1482)gaa>ga		chromosome 2 open reading frame 71																																				SO:0001651	inframe_deletion	388939				response to stimulus|visual perception	photoreceptor outer segment		g.chr2:29295647_29295649delTCC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1479_1481delGGA	2.37:g.29295656_29295658delTCC	ENSP00000332809:p.Glu494del						p.EE493del	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN			1	1478_1480	-			493						In_Frame_Del	DEL	ENST00000331664.5	37	c.1479_1481delGGA	CCDS42669.1																																																																																				0.542	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		8	1004						8	1004	---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54093344	54093345	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:54093344_54093345insT	ENST00000404125.1	-	46	5468_5469	c.5413_5414insA	c.(5413-5415)accfs	p.T1805fs	PSME4_ENST00000421748.2_Frame_Shift_Ins_p.T949fs|PSME4_ENST00000476586.1_5'UTR	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1805					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.T1691fs*>39(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ATTGGATAAGGTTTTTTTTACA	0.401																																						ENST00000404125.1																			1	Deletion - Frameshift(1)	p.T1691fs*>39(1)	ovary(1)	breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60						c.(5413-5415)cttfs		proteasome (prosome, macropain) activator subunit 4																																				SO:0001589	frameshift_variant	23198				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding	g.chr2:54093344_54093345insT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.5414dupA	2.37:g.54093352_54093352dupT	ENSP00000384211:p.Thr1805fs					PSME4_ENST00000476586.1_5'UTR|PSME4_ENST00000421748.2_Frame_Shift_Ins_p.L949fs	p.L1805fs	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)		46	5468_5469	-			1805					Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Frame_Shift_Ins	INS	ENST00000404125.1	37	c.5413_5414insA	CCDS33197.2																																																																																				0.401	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		8	876						8	876	---	---	---	---
LINC01122	400955	broad.mit.edu	37	2	58688842	58688843	+	lincRNA	DEL	CT	CT	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:58688842_58688843delCT	ENST00000452840.1	+	0	127																											TCTCTGCTAGCTCTCTCTCTCT	0.465																																						ENST00000452840.1																			0																																																			0							g.chr2:58688842_58688843delCT																													2.37:g.58688852_58688853delCT														0	127	+									RNA	DEL	ENST00000452840.1	37																																																																																						0.465	AC007092.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000327022.1			8	293						8	293	---	---	---	---
LOC101927533	101927533	broad.mit.edu	37	2	65738863	65738863	+	lincRNA	DEL	G	G	-	rs373784983|rs377731020		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:65738863delG	ENST00000377977.3	+	0	862																											TTTTTTTTTTGTCCAGGAGGC	0.303																																						ENST00000377977.3																			0																																																			0							g.chr2:65738863delG																													2.37:g.65738863delG														0	862	+									RNA	DEL	ENST00000377977.3	37																																																																																						0.303	AC074391.1-010	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470883.1			13	20						13	20	---	---	---	---
IGKV1D-8	28904	broad.mit.edu	37	2	90259860	90259861	+	RNA	INS	-	-	C			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:90259860_90259861insC	ENST00000471857.1	+	0	236									immunoglobulin kappa variable 1D-8																		AATTTACTCAGCCAATGTGCTC	0.48																																						ENST00000471857.1																			0																																																			0							g.chr2:90259860_90259861insC	Z00008		2p11.2	2012-02-08			ENSG00000239819	ENSG00000239819		"""Immunoglobulins / IGK locus"""	5759	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000151570		2.37:g.90259862_90259862dupC														0	236	+									RNA	INS	ENST00000471857.1	37																																																																																						0.480	IGKV1D-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323145.2	NG_000833		10	919						10	919	---	---	---	---
MRPS5	64969	broad.mit.edu	37	2	95775728	95775728	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:95775728delT	ENST00000272418.2	-	4	544	c.336delA	c.(334-336)aaafs	p.K112fs		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	112					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						TGCCTCTTCCTTTTTTTGCTC	0.383																																						ENST00000272418.2																			0				central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						c.(334-336)aafs		mitochondrial ribosomal protein S5							100.0	103.0	102.0					2																	95775728		2203	4300	6503	SO:0001589	frameshift_variant	64969				translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome	g.chr2:95775728delT	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.336delA	2.37:g.95775728delT	ENSP00000272418:p.Lys112fs						p.K112fs	NM_031902.3	NP_114108.1	P82675	RT05_HUMAN			4	544	-			112					Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Frame_Shift_Del	DEL	ENST00000272418.2	37	c.336delA	CCDS2010.1																																																																																				0.383	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902		9	929						9	929	---	---	---	---
ITPRIPL1	150771	broad.mit.edu	37	2	96992793	96992795	+	In_Frame_Del	DEL	GAG	GAG	-	rs368798001		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:96992793_96992795delGAG	ENST00000439118.2	+	3	675_677	c.424_426delGAG	c.(424-426)gagdel	p.E147del	ITPRIPL1_ENST00000536814.1_In_Frame_Del_p.E139del|ITPRIPL1_ENST00000542887.1_In_Frame_Del_p.E139del|ITPRIPL1_ENST00000361124.4_In_Frame_Del_p.E155del	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	147						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TTCCAGCAGTGAGGAGGAGGAGG	0.532																																						ENST00000361124.4																			0				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(448-450)del		inositol 1,4,5-trisphosphate receptor interacting protein-like 1																																				SO:0001651	inframe_deletion	150771					integral to membrane		g.chr2:96992793_96992795delGAG		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.424_426delGAG	2.37:g.96992802_96992804delGAG	ENSP00000389308:p.Glu147del					ITPRIPL1_ENST00000439118.2_In_Frame_Del_p.E147del|ITPRIPL1_ENST00000542887.1_In_Frame_Del_p.E139del|ITPRIPL1_ENST00000536814.1_In_Frame_Del_p.E139del	p.E155del	NM_178495.5	NP_848590.3	Q6GPH6	IPIL1_HUMAN			1	859_861	+			147					F5H1L8|Q8NE61	In_Frame_Del	DEL	ENST00000439118.2	37	c.448_450delGAG	CCDS46360.1																																																																																				0.532	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495		9	509						9	509	---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98427639	98427639	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:98427639delT	ENST00000186436.5	-	18	2148	c.1920delA	c.(1918-1920)aaafs	p.K640fs		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	640						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TCCCCTCTAATTTTTTTGCAG	0.393																																						ENST00000186436.5																			0				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						c.(1918-1920)aafs		transmembrane protein 131							277.0	265.0	269.0					2																	98427639		1831	4095	5926	SO:0001589	frameshift_variant	23505					integral to membrane		g.chr2:98427639delT	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.1920delA	2.37:g.98427639delT	ENSP00000186436:p.Lys640fs						p.K640fs	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN			18	2148	-			640						Frame_Shift_Del	DEL	ENST00000186436.5	37	c.1920delA	CCDS46368.1																																																																																				0.393	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		11	1565						11	1565	---	---	---	---
IL1R2	7850	broad.mit.edu	37	2	102638648	102638649	+	Splice_Site	INS	-	-	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:102638648_102638649insA	ENST00000332549.3	+	6	917_918		c.e6-1		IL1R2_ENST00000393414.2_Splice_Site|IL1R2_ENST00000441002.1_Splice_Site	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II						cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						ATCTTTCTCAGAAAAAAAAGAA	0.441																																					Pancreas(106;189 1628 2302 5133 12295)	ENST00000332549.3																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						c.e6-1		interleukin 1 receptor, type II	Anakinra(DB00026)																																			SO:0001630	splice_region_variant	7850				immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity	g.chr2:102638648_102638649insA	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.689-1->A	2.37:g.102638656_102638656dupA						IL1R2_ENST00000393414.2_Splice_Site|IL1R2_ENST00000441002.1_Splice_Site		NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN			6	917_918	+								D3DVJ5|Q6LCE6|Q9UE68	Splice_Site	INS	ENST00000332549.3	37		CCDS2054.1																																																																																				0.441	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	Intron	8	908						8	908	---	---	---	---
SLC9A4	389015	broad.mit.edu	37	2	103149137	103149137	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:103149137delA	ENST00000295269.4	+	12	2844	c.2387delA	c.(2386-2388)caafs	p.Q796fs		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	796					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCTTTGCTCCAAAAAAAATAG	0.473																																						ENST00000295269.4																			0				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						c.(2386-2388)cafs		solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4							43.0	37.0	39.0					2																	103149137		2203	4300	6503	SO:0001589	frameshift_variant	389015				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity	g.chr2:103149137delA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2387delA	2.37:g.103149137delA	ENSP00000295269:p.Gln796fs						p.Q796fs	NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN			12	2844	+			796					Q69YK0	Frame_Shift_Del	DEL	ENST00000295269.4	37	c.2387delA	CCDS33264.1																																																																																				0.473	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		10	233						10	233	---	---	---	---
SULT1C3	442038	broad.mit.edu	37	2	108863685	108863685	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:108863685delA	ENST00000329106.2	+	1	35	c.35delA	c.(34-36)gaafs	p.E12fs	SULT1C3_ENST00000376700.1_Frame_Shift_Del_p.E12fs	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3	12					sulfur compound metabolic process (GO:0006790)	cytoplasm (GO:0005737)	alcohol sulfotransferase activity (GO:0004027)|aryl sulfotransferase activity (GO:0004062)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						CCCACGATGGAAAAAAAGCCA	0.353																																						ENST00000329106.2																			0				breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						c.(34-36)gafs		sulfotransferase family, cytosolic, 1C, member 3							90.0	96.0	94.0					2																	108863685		2203	4300	6503	SO:0001589	frameshift_variant	442038					cytoplasm	alcohol sulfotransferase activity	g.chr2:108863685delA	BC146362	CCDS33267.1	2q12.3	2007-07-26			ENSG00000196228	ENSG00000196228		"""Sulfotransferases, cytosolic"""	33543	protein-coding gene	gene with protein product						14676822, 17425406	Standard	NM_001008743		Approved		uc010ywo.2	Q6IMI6	OTTHUMG00000153227	ENST00000329106.2:c.35delA	2.37:g.108863685delA	ENSP00000333310:p.Glu12fs					SULT1C3_ENST00000376700.1_Frame_Shift_Del_p.E12fs	p.E12fs	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN			1	35	+			12					Q6IMI5	Frame_Shift_Del	DEL	ENST00000329106.2	37	c.35delA	CCDS33267.1																																																																																				0.353	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743		10	700						10	700	---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109380485	109380487	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:109380485_109380487delGAT	ENST00000283195.6	+	20	3616_3618	c.3490_3492delGAT	c.(3490-3492)gatdel	p.D1168del		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1168					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGCCCATGGGGATGATGATGATG	0.424																																						ENST00000283195.6																		RANBP2/ALK(34)	0				NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						c.(3490-3492)del		RAN binding protein 2																																				SO:0001651	inframe_deletion	5903				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding	g.chr2:109380485_109380487delGAT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3490_3492delGAT	2.37:g.109380494_109380496delGAT	ENSP00000283195:p.Asp1168del						p.D1168del	NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN			20	3616_3618	+			1168					Q13074|Q15280|Q53TE2|Q59FH7	In_Frame_Del	DEL	ENST00000283195.6	37	c.3490_3492delGAT	CCDS2079.1																																																																																				0.424	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		8	961						8	961	---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167055992	167055992	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:167055992delT	ENST00000409435.1	-	26	5156	c.5157delA	c.(5155-5157)aaafs	p.K1719fs	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.K1720fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.K1708fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.K1720fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1719					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAGGATGAACTTTTTTTGGGT	0.423																																						ENST00000375387.4																			0				NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108						c.(5158-5160)aafs		sodium channel, voltage-gated, type IX, alpha subunit	Lamotrigine(DB00555)|Lidocaine(DB00281)						234.0	251.0	245.0					2																	167055992		2201	4300	6501	SO:0001589	frameshift_variant	6335					voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr2:167055992delT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.5157delA	2.37:g.167055992delT	ENSP00000386330:p.Lys1719fs					SCN9A_ENST00000409672.1_Frame_Shift_Del_p.K1708fs|SCN9A_ENST00000409435.1_Frame_Shift_Del_p.K1719fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.K1720fs	p.K1720fs			Q15858	SCN9A_HUMAN			27	5500	-			1719					A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	c.5160delA	CCDS46441.1																																																																																				0.423	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		10	1952						10	1952	---	---	---	---
RBM45	129831	broad.mit.edu	37	2	178988920	178988920	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:178988920delA	ENST00000286070.5	+	8	1227	c.1135delA	c.(1135-1137)aaafs	p.K381fs		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	383					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A382fs*7(2)|p.?(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TCCATCATGCAAAAAAAAAGC	0.353																																						ENST00000286070.5																			3	Deletion - Frameshift(2)|Unknown(1)	p.A382fs*7(2)|p.?(1)	large_intestine(2)|skin(1)	endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						c.(1135-1137)aafs		RNA binding motif protein 45				3,107,4156		0,0,3,40,27,2063	69.0	75.0	73.0			4.7	1.0	2		75	6,163,8085		0,0,6,55,53,4013	no	codingComplex	RBM45	NM_152945.2		0,0,9,95,80,6076	A1A1,A1A2,A1R,A2A2,A2R,RR		2.0475,2.5785,2.2284			178988920	9,270,12241	2203	4300	6503	SO:0001589	frameshift_variant	129831				cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding	g.chr2:178988920delA	AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"""RNA binding motif (RRM) containing"""	24468	protein-coding gene	gene with protein product	"""developmentally regulated RNA binding protein 1"""	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.1135delA	2.37:g.178988920delA	ENSP00000286070:p.Lys381fs						p.K381fs	NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)		8	1227	+			383					Q6NYL0|Q8NFC9	Frame_Shift_Del	DEL	ENST00000286070.5	37	c.1135delA	CCDS33335.1																																																																																				0.353	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		9	582						9	582	---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197943383	197943384	+	Frame_Shift_Del	DEL	TG	TG	-	rs139294990		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:197943383_197943384delTG	ENST00000409153.1	-	16	1875_1876	c.1693_1694delCA	c.(1693-1695)catfs	p.H565fs	ANKRD44_ENST00000450567.1_Intron|ANKRD44_ENST00000539527.1_Frame_Shift_Del_p.H493fs|ANKRD44_ENST00000337207.5_Intron|ANKRD44_ENST00000328737.2_Intron|ANKRD44_ENST00000282272.8_Intron			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	0										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTTGGGGTATGTGTGTGTGTG	0.411																																						ENST00000409153.1																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45						c.(1693-1695)tfs		ankyrin repeat domain 44																																				SO:0001589	frameshift_variant	91526						protein binding	g.chr2:197943383_197943384delTG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000409153.1:c.1693_1694delCA	2.37:g.197943393_197943394delTG	ENSP00000387141:p.His565fs					ANKRD44_ENST00000282272.8_Intron|ANKRD44_ENST00000328737.2_Intron|ANKRD44_ENST00000337207.5_Intron|ANKRD44_ENST00000539527.1_Frame_Shift_Del_p.H493fs|ANKRD44_ENST00000450567.1_Intron	p.H565fs			Q8N8A2	ANR44_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)		16	1875_1876	-			811					Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Frame_Shift_Del	DEL	ENST00000409153.1	37	c.1693_1694delCA																																																																																					0.411	ANKRD44-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335114.3	NM_153697		8	84						8	84	---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202352352	202352352	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:202352352delT	ENST00000286195.3	-	15	1899	c.1855delA	c.(1855-1857)attfs	p.I619fs	ALS2CR11_ENST00000439802.1_3'UTR|ALS2CR11_ENST00000439140.1_Frame_Shift_Del_p.I1816fs|ALS2CR11_ENST00000482942.1_5'Flank	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	619										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CCTCTTTTAATTTTTTTTGGC	0.323																																						ENST00000439140.1																			0				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						c.(5446-5448)ttfs		amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11							97.0	96.0	96.0					2																	202352352		2203	4300	6503	SO:0001589	frameshift_variant	151254							g.chr2:202352352delT	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1855delA	2.37:g.202352352delT	ENSP00000286195:p.Ile619fs					ALS2CR11_ENST00000439802.1_3'UTR|ALS2CR11_ENST00000286195.3_Frame_Shift_Del_p.I619fs	p.I1816fs	NM_001168221.1	NP_001161693.1	Q53TS8	AL2SA_HUMAN			16	5490	-			619					C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Frame_Shift_Del	DEL	ENST00000286195.3	37	c.5446delA	CCDS2349.1																																																																																				0.323	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		9	560						9	560	---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207174869	207174869	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:207174869delA	ENST00000374423.3	+	5	6003	c.5617delA	c.(5617-5619)aaafs	p.K1875fs		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1875							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						TTCGAAGGGGAAAAAAAAGGT	0.413																																						ENST00000374423.3																			0				endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						c.(5617-5619)aafs		zinc finger, DBF-type containing 2							58.0	57.0	57.0					2																	207174869		1921	4134	6055	SO:0001589	frameshift_variant	57683						nucleic acid binding|zinc ion binding	g.chr2:207174869delA	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.5617delA	2.37:g.207174869delA	ENSP00000363545:p.Lys1875fs						p.K1875fs	NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN			5	6003	+			1875					Q6ZNP7|Q6ZSN8	Frame_Shift_Del	DEL	ENST00000374423.3	37	c.5617delA	CCDS46501.1																																																																																				0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		7	262						7	262	---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	214012392	214012393	+	Intron	DEL	AC	AC	-	rs372594237		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:214012392_214012393delAC	ENST00000434687.1	-	4	449				IKZF2_ENST00000451136.2_Intron|IKZF2_ENST00000342002.2_Intron|IKZF2_ENST00000421754.2_Intron|IKZF2_ENST00000374319.4_Intron|IKZF2_ENST00000442445.1_Frame_Shift_Del_p.V66fs|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000457361.1_Intron|IKZF2_ENST00000413091.3_Intron			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)						positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		TGCTGGAGAGACACACACACAC	0.401																																						ENST00000442445.1																			0				NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(196-198)cfs		IKAROS family zinc finger 2 (Helios)																																				SO:0001627	intron_variant	22807				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr2:214012392_214012393delAC	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13177	protein-coding gene	gene with protein product		606234	"""zinc finger protein, subfamily 1A, 2 (Helios)"""	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.139+38GT>-	2.37:g.214012402_214012403delAC						IKZF2_ENST00000413091.3_Intron|IKZF2_ENST00000374319.4_Intron|IKZF2_ENST00000434687.1_Intron|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000451136.2_Intron|IKZF2_ENST00000421754.2_Intron|IKZF2_ENST00000342002.2_Intron|IKZF2_ENST00000457361.1_Intron	p.V66fs			Q9UKS7	IKZF2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)	3	253_254	-		Esophageal squamous(248;0.0559)|Renal(323;0.218)	0					Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Frame_Shift_Del	DEL	ENST00000434687.1	37	c.196_197delGT	CCDS2395.1																																																																																				0.401	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260		15	550						15	550	---	---	---	---
EFHD1	80303	broad.mit.edu	37	2	233546363	233546365	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr2:233546363_233546365delGGA	ENST00000264059.3	+	4	1131_1133	c.654_656delGGA	c.(652-657)cgggag>cgg	p.E222del	snoU13_ENST00000459149.1_RNA|EFHD1_ENST00000409708.1_In_Frame_Del_p.E110del|EFHD1_ENST00000409613.1_In_Frame_Del_p.E126del|EFHD1_ENST00000410095.1_In_Frame_Del_p.E110del	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	222					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		AGCGGAAGCGGGAGGAGGAGGAG	0.547																																						ENST00000264059.3																			0				NS(1)|breast(1)|large_intestine(2)|lung(3)	7						c.(652-657)cgg>cg		EF-hand domain family, member D1																																				SO:0001651	inframe_deletion	80303						calcium ion binding|protein binding	g.chr2:233546363_233546365delGGA		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.654_656delGGA	2.37:g.233546372_233546374delGGA	ENSP00000264059:p.Glu222del					EFHD1_ENST00000410095.1_In_Frame_Del_p.RE106del|EFHD1_ENST00000409613.1_In_Frame_Del_p.RE122del|EFHD1_ENST00000409708.1_In_Frame_Del_p.RE106del	p.RE218del	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)	4	1131_1133	+		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)	218					B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	In_Frame_Del	DEL	ENST00000264059.3	37	c.654_656delGGA	CCDS2497.1																																																																																				0.547	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		7	658						7	658	---	---	---	---
EDEM1	9695	broad.mit.edu	37	3	5248941	5248941	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:5248941delT	ENST00000256497.4	+	7	1454	c.1321delT	c.(1321-1323)tttfs	p.F442fs	EDEM1_ENST00000445686.1_Frame_Shift_Del_p.F247fs	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	442					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TCTGCAGGCCTTTTTCCCTGG	0.463																																						ENST00000256497.4																			0				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						c.(1321-1323)ttfs		ER degradation enhancer, mannosidase alpha-like 1							155.0	149.0	151.0					3																	5248941		2203	4300	6503	SO:0001589	frameshift_variant	9695				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding	g.chr3:5248941delT	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1321delT	3.37:g.5248941delT	ENSP00000256497:p.Phe442fs					EDEM1_ENST00000445686.1_Frame_Shift_Del_p.F247fs	p.F442fs	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN		Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)	7	1454	+			442					A8K9C8|B4DXP3	Frame_Shift_Del	DEL	ENST00000256497.4	37	c.1321delT	CCDS33686.1																																																																																				0.463	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		8	632						8	632	---	---	---	---
TMEM40	55287	broad.mit.edu	37	3	12790198	12790200	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:12790198_12790200delGAG	ENST00000314124.7	-	3	521_523	c.165_167delCTC	c.(163-168)tcctct>tct	p.55_56SS>S	TMEM40_ENST00000431022.2_In_Frame_Del_p.71_72SS>S|TMEM40_ENST00000264728.8_In_Frame_Del_p.55_56SS>S|TMEM40_ENST00000435218.2_In_Frame_Del_p.55_56SS>S|TMEM40_ENST00000435575.1_Intron	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	55	Ser-rich.			S -> F (in Ref. 1; BAA91967). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						tgaggaggaagaggaggaggagg	0.419																																						ENST00000314124.7																			0				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						c.(163-168)tct>tc		transmembrane protein 40																																				SO:0001651	inframe_deletion	55287					integral to membrane		g.chr3:12790198_12790200delGAG	BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726			25620	protein-coding gene	gene with protein product						12477932	Standard	NM_018306		Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.165_167delCTC	3.37:g.12790207_12790209delGAG	ENSP00000322837:p.Ser70del					TMEM40_ENST00000264728.8_In_Frame_Del_p.SS69del|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000435218.2_In_Frame_Del_p.SS69del|TMEM40_ENST00000431022.2_In_Frame_Del_p.SS85del	p.SS69del	NM_018306.2	NP_060776.2	Q8WWA1	TMM40_HUMAN			3	521_523	-			69			Ser-rich.		C9JID5|Q8NAL4|Q9NUZ4	In_Frame_Del	DEL	ENST00000314124.7	37	c.165_167delCTC	CCDS2613.1																																																																																				0.419	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252029.2	NM_018306		7	875						7	875	---	---	---	---
SGOL1	151648	broad.mit.edu	37	3	20216049	20216050	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:20216049_20216050insT	ENST00000263753.4	-	6	1112_1113	c.973_974insA	c.(973-975)atgfs	p.M325fs	SGOL1_ENST00000443724.1_Intron|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000383774.1_Intron|SGOL1_ENST00000421451.1_Frame_Shift_Ins_p.M325fs|SGOL1_ENST00000419233.2_Intron|SGOL1_ENST00000425061.1_Intron|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000412997.1_Frame_Shift_Ins_p.M325fs|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000417364.1_Intron|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000437051.1_Intron|SGOL1_ENST00000412868.1_Frame_Shift_Ins_p.M325fs	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	325					attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						AGATTTGTGCATTTTTTTTTGG	0.317																																						ENST00000412997.1																			0				kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						c.(973-975)gcafs		shugoshin-like 1 (S. pombe)																																				SO:0001589	frameshift_variant	151648				attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding	g.chr3:20216049_20216050insT	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.974dupA	3.37:g.20216058_20216058dupT	ENSP00000263753:p.Met325fs					SGOL1_ENST00000421451.1_Frame_Shift_Ins_p.A325fs|SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000437051.1_Intron|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000425061.1_Intron|SGOL1_ENST00000412868.1_Frame_Shift_Ins_p.A325fs|SGOL1_ENST00000263753.4_Frame_Shift_Ins_p.A325fs|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000417364.1_Intron|SGOL1_ENST00000419233.2_Intron|SGOL1_ENST00000443724.1_Intron|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000383774.1_Intron|SGOL1-AS1_ENST00000448208.1_RNA	p.A325fs	NM_001199251.1	NP_001186180.1	Q5FBB7	SGOL1_HUMAN			6	1324_1325	-			325					Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Frame_Shift_Ins	INS	ENST00000263753.4	37	c.973_974insA	CCDS33716.1																																																																																				0.317	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484		9	215						9	215	---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33602361	33602361	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:33602361delT	ENST00000468888.2	-	28	2939	c.2893delA	c.(2893-2895)atgfs	p.M965fs	CLASP2_ENST00000480013.1_Frame_Shift_Del_p.M744fs|CLASP2_ENST00000461133.3_Frame_Shift_Del_p.M724fs|CLASP2_ENST00000539981.1_Frame_Shift_Del_p.M734fs|CLASP2_ENST00000399362.4_Frame_Shift_Del_p.M964fs|CLASP2_ENST00000359576.5_Frame_Shift_Del_p.M956fs|CLASP2_ENST00000307312.7_Frame_Shift_Del_p.M446fs			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	745	Interaction with RSN and localization to the Golgi and kinetochores.				axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCAGCACCCATTTTTTTTAGT	0.343																																						ENST00000399362.4																			0				breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(2890-2892)tgfs		cytoplasmic linker associated protein 2							188.0	194.0	192.0					3																	33602361		1841	4103	5944	SO:0001589	frameshift_variant	23122							g.chr3:33602361delT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.2893delA	3.37:g.33602361delT	ENSP00000419974:p.Met965fs					CLASP2_ENST00000539981.1_Frame_Shift_Del_p.M734fs|CLASP2_ENST00000468888.2_Frame_Shift_Del_p.M965fs|CLASP2_ENST00000359576.5_Frame_Shift_Del_p.M956fs|CLASP2_ENST00000461133.3_Frame_Shift_Del_p.M724fs|CLASP2_ENST00000307312.7_Frame_Shift_Del_p.M446fs|CLASP2_ENST00000480013.1_Frame_Shift_Del_p.M744fs	p.M964fs	NM_015097.2	NP_055912.2	B2RTR1	B2RTR1_HUMAN			28	3243	-			966					Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Frame_Shift_Del	DEL	ENST00000468888.2	37	c.2890delA																																																																																					0.343	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		13	658						13	658	---	---	---	---
ACAA1	30	broad.mit.edu	37	3	38162039	38162040	+	IGR	DEL	GA	GA	-	rs140494598		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:38162039_38162040delGA	ENST00000333167.8	-	0	1785				DLEC1_ENST00000452631.2_Frame_Shift_Del_p.G1605fs|DLEC1_ENST00000346219.3_Frame_Shift_Del_p.G1602fs|ACAA1_ENST00000480865.1_5'Flank|DLEC1_ENST00000308059.6_Frame_Shift_Del_p.G1602fs	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		AGTGCGAGTGGAGAGAGAGAGA	0.579																																						ENST00000308059.6																			0				NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51						c.(4804-4806)gfs		deleted in lung and esophageal cancer 1																																				SO:0001628	intergenic_variant	9940				negative regulation of cell proliferation	cytoplasm		g.chr3:38162039_38162040delGA	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		3.37:g.38162049_38162050delGA						DLEC1_ENST00000346219.3_Frame_Shift_Del_p.G1602fs|DLEC1_ENST00000452631.2_Frame_Shift_Del_p.G1605fs	p.G1602fs			Q9Y238	DLEC1_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)	34	4826_4827	+			1602					G5E935|Q96CA6	Frame_Shift_Del	DEL	ENST00000333167.8	37	c.4805_4806delGA	CCDS2673.1																																																																																				0.579	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		7	298						7	298	---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71247357	71247359	+	In_Frame_Del	DEL	TGC	TGC	-	rs370638902		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:71247357_71247359delTGC	ENST00000318789.4	-	6	699_701	c.174_176delGCA	c.(172-177)cagcaa>caa	p.58_59QQ>Q	FOXP1_ENST00000318779.3_In_Frame_Del_p.58_59QQ>Q|FOXP1_ENST00000475937.1_In_Frame_Del_p.58_59QQ>Q|FOXP1_ENST00000484350.1_In_Frame_Del_p.58_59QQ>Q|FOXP1_ENST00000498215.1_In_Frame_Del_p.58_59QQ>Q|FOXP1_ENST00000493089.1_In_Frame_Del_p.58_59QQ>Q|FOXP1_ENST00000468577.1_In_Frame_Del_p.58_59QQ>Q	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	58	Gln-rich.	Breakpoint for translocation to form PAX5-FOXP1.			negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CAGTACCTGTTGCTGCTGCTGCT	0.586			T	PAX5	ALL																																	ENST00000318789.4				Dom	yes		3	3p14.1	27086	T	forkhead box P1			L	PAX5		ALL		0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						c.(172-177)caa>ca		forkhead box P1																																				SO:0001651	inframe_deletion	27086				cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding	g.chr3:71247357_71247359delTGC	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.174_176delGCA	3.37:g.71247366_71247368delTGC	ENSP00000318902:p.Gln60del					FOXP1_ENST00000484350.1_In_Frame_Del_p.QQ58del|FOXP1_ENST00000318779.3_In_Frame_Del_p.QQ58del|FOXP1_ENST00000468577.1_In_Frame_Del_p.QQ58del|FOXP1_ENST00000498215.1_In_Frame_Del_p.QQ58del|FOXP1_ENST00000475937.1_In_Frame_Del_p.QQ58del|FOXP1_ENST00000493089.1_In_Frame_Del_p.QQ58del	p.QQ58del	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)	6	699_701	-		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)	58			Gln-rich.		A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	In_Frame_Del	DEL	ENST00000318789.4	37	c.174_176delGCA	CCDS2914.1																																																																																				0.586	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		8	506						8	506	---	---	---	---
VGLL3	389136	broad.mit.edu	37	3	87027857	87027859	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:87027857_87027859delCTC	ENST00000398399.2	-	2	583_585	c.220_222delGAG	c.(220-222)gagdel	p.E74del	VGLL3_ENST00000383698.3_In_Frame_Del_p.E74del	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GCTGGtctttctcctcctcctcc	0.502																																						ENST00000398399.2																			0				NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19						c.(220-222)del		vestigial like 3 (Drosophila)				1,38,3879		0,0,1,6,26,1926						5.1	1.0			64	3,85,7944		0,0,3,22,41,3950	no	codingComplex	VGLL3	NM_016206.2		0,0,4,28,67,5876	A1A1,A1A2,A1R,A2A2,A2R,RR		1.0956,0.9954,1.0628				4,123,11823				SO:0001651	inframe_deletion	389136				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr3:87027857_87027859delCTC	AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"""vestigial like 3 (Drosophila)"""			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.220_222delGAG	3.37:g.87027866_87027868delCTC	ENSP00000381436:p.Glu74del					VGLL3_ENST00000383698.3_In_Frame_Del_p.E74del	p.E74del	NM_016206.2	NP_057290.2	A8MV65	VGLL3_HUMAN		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)	2	583_585	-	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)	74						In_Frame_Del	DEL	ENST00000398399.2	37	c.220_222delGAG	CCDS43110.1																																																																																				0.502	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206		7	259						7	259	---	---	---	---
SDHAP1	255812	broad.mit.edu	37	3	195713385	195713386	+	RNA	INS	-	-	T	rs199843390		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr3:195713385_195713386insT	ENST00000427841.1	-	0	176					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		AAAGCATGAACTTACGGAATCT	0.401																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195713385_195713386insT	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195713387_195713387dupT								NR_003264.2						0	176	-									RNA	INS	ENST00000427841.1	37																																																																																						0.401	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			22	61						22	61	---	---	---	---
OTOP1	133060	broad.mit.edu	37	4	4204225	4204229	+	Frame_Shift_Del	DEL	TTGAG	TTGAG	-	rs369956607		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:4204225_4204229delTTGAG	ENST00000296358.4	-	4	700_704	c.676_680delCTCAA	c.(676-681)ctcaatfs	p.LN226fs		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	226					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.L226fs*1(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTTGTGCTCATTGAGTTGGTGCTTT	0.502																																						ENST00000296358.4																			1	Deletion - Frameshift(1)	p.L226fs*1(1)	liver(1)	NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						c.(676-681)tfs		otopetrin 1																																				SO:0001589	frameshift_variant	133060				biomineral tissue development	extracellular space|integral to membrane		g.chr4:4204225_4204229delTTGAG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.676_680delCTCAA	4.37:g.4204225_4204229delTTGAG	ENSP00000296358:p.Leu226fs						p.LN226fs	NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	4	700_704	-			226					A1L476	Frame_Shift_Del	DEL	ENST00000296358.4	37	c.676_680delCTCAA	CCDS3372.1																																																																																				0.502	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		7	555						7	555	---	---	---	---
PROM1	8842	broad.mit.edu	37	4	15995680	15995680	+	Frame_Shift_Del	DEL	T	T	-	rs376676164		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:15995680delT	ENST00000510224.1	-	16	1945	c.1697delA	c.(1696-1698)aatfs	p.N566fs	PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000505450.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs			O43490	PROM1_HUMAN	prominin 1	566					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						AGTGCCTCTATTTTTTTTGCA	0.428																																						ENST00000505450.1																			0				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						c.(1669-1671)atfs		prominin 1							189.0	187.0	188.0					4																	15995680		1901	4120	6021	SO:0001589	frameshift_variant	8842				camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding	g.chr4:15995680delT	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1697delA	4.37:g.15995680delT	ENSP00000426809:p.Asn566fs					PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000510224.1_Frame_Shift_Del_p.N566fs	p.N557fs	NM_001145848.1	NP_001139320.1	O43490	PROM1_HUMAN			15	2282	-			566					Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Frame_Shift_Del	DEL	ENST00000510224.1	37	c.1670delA	CCDS47029.1																																																																																				0.428	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		12	416						12	416	---	---	---	---
GABRG1	2565	broad.mit.edu	37	4	46060358	46060358	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:46060358delA	ENST00000295452.4	-	7	959	c.792delT	c.(790-792)tttfs	p.F264fs		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	264					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.F264fs*3(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCTCAGGTCAAAAAAAATTG	0.294																																						ENST00000295452.4																			1	Deletion - Frameshift(1)	p.F264fs*3(1)	large_intestine(1)	breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						c.(790-792)ttfs		gamma-aminobutyric acid (GABA) A receptor, gamma 1							94.0	97.0	96.0					4																	46060358		2203	4300	6503	SO:0001589	frameshift_variant	2565				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity	g.chr4:46060358delA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.792delT	4.37:g.46060358delA	ENSP00000295452:p.Phe264fs						p.F264fs	NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN		Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	7	959	-			264					Q5H9T8	Frame_Shift_Del	DEL	ENST00000295452.4	37	c.792delT	CCDS3470.1																																																																																				0.294	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		8	363						8	363	---	---	---	---
CXXC4	80319	broad.mit.edu	37	4	105412465	105412467	+	5'UTR	DEL	GCC	GCC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:105412465_105412467delGCC	ENST00000426831.1	-	0	0_2				AC004053.1_ENST00000500179.1_RNA|CXXC4_ENST00000394767.2_In_Frame_Del_p.G165del|CXXC4_ENST00000466963.1_Intron|AC093628.1_ENST00000606234.1_RNA			Q9H2H0	CXXC4_HUMAN	CXXC finger protein 4						negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)	DNA binding (GO:0003677)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)		TGGTCCTgctgccgccgccgccg	0.695																																						ENST00000394767.2																			0				kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						c.(493-495)del		CXXC finger protein 4																																				SO:0001623	5_prime_UTR_variant	80319				negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding	g.chr4:105412465_105412467delGCC		CCDS3665.1, CCDS3665.2	4q22-q24	2014-02-18	2011-12-01		ENSG00000168772	ENSG00000168772			24593	protein-coding gene	gene with protein product	"""Dvl-binding protein IDAX (inhibition of the Dvl and Axin complex)"""	611645				11113207	Standard	NM_025212		Approved	IDAX	uc003hxf.2	Q9H2H0	OTTHUMG00000131121	ENST00000426831.1:c.-15GGC>-	4.37:g.105412474_105412476delGCC						CXXC4_ENST00000466963.1_Intron|CXXC4_ENST00000426831.1_5'UTR|AC004053.1_ENST00000500179.1_RNA	p.G165del	NM_025212.2	NP_079488.2	Q9H2H0	CXXC4_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)	2	943_945	-			0			Interaction with DVL1 (By similarity).			In_Frame_Del	DEL	ENST00000426831.1	37	c.493_495delGGC																																																																																					0.695	CXXC4-201	KNOWN	basic	protein_coding	protein_coding		NM_025212		9	360						9	360	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140810639	140810641	+	In_Frame_Del	DEL	GCT	GCT	-	rs372496848		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:140810639_140810641delGCT	ENST00000509479.2	-	2	2805_2807	c.1949_1951delAGC	c.(1948-1953)cagccg>ccg	p.Q650del	MAML3_ENST00000327122.5_In_Frame_Del_p.Q494del|MAML3_ENST00000398940.1_In_Frame_Del_p.Q178del	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					GGAGGTGGCGgctgctgctgctg	0.586																																						ENST00000509479.2																			0				breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25						c.(1948-1953)ccg>c		mastermind-like 3 (Drosophila)																																				SO:0001651	inframe_deletion	55534				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity	g.chr4:140810639_140810641delGCT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1949_1951delAGC	4.37:g.140810648_140810650delGCT	ENSP00000421180:p.Gln650del					MAML3_ENST00000327122.5_In_Frame_Del_p.QP494del|MAML3_ENST00000398940.1_In_Frame_Del_p.QP178del	p.QP650del	NM_018717.4	NP_061187.2	Q96JK9	MAML3_HUMAN			2	2805_2807	-	all_hematologic(180;0.162)		646			Gln-rich.			In_Frame_Del	DEL	ENST00000509479.2	37	c.1949_1951delAGC	CCDS54805.1																																																																																				0.586	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			9	297						9	297	---	---	---	---
LOC100505685	100505685	broad.mit.edu	37	4	152880686	152880688	+	RNA	DEL	TGC	TGC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:152880686_152880688delTGC	ENST00000515329.1	+	0	266																											CACctgctgttgctgctgctgct	0.542																																						ENST00000515329.1																			0																																																			0							g.chr4:152880686_152880688delTGC																													4.37:g.152880695_152880697delTGC														0	266	+									RNA	DEL	ENST00000515329.1	37																																																																																						0.542	RP11-73G16.1-001	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000365880.2			2	4						2	4	---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186544620	186544622	+	In_Frame_Del	DEL	GGT	GGT	-	rs562339021		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr4:186544620_186544622delGGT	ENST00000284776.7	-	13	2458_2460	c.1949_1951delACC	c.(1948-1953)caccgc>cgc	p.H650del	SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000355634.5_In_Frame_Del_p.H750del|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000418609.1_In_Frame_Del_p.H554del|SORBS2_ENST00000431808.1_In_Frame_Del_p.H650del|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	650	His-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		ATGAggtggcggtggtggtggtg	0.522																																					Esophageal Squamous(153;41 2433 9491 36028)	ENST00000431808.1																			0				endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53						c.(1948-1953)cgc>c		sorbin and SH3 domain containing 2																																				SO:0001651	inframe_deletion	8470					actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding	g.chr4:186544620_186544622delGGT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1949_1951delACC	4.37:g.186544629_186544631delGGT	ENSP00000284776:p.His650del					SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000284776.7_In_Frame_Del_p.HR650del|SORBS2_ENST00000418609.1_In_Frame_Del_p.HR554del|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000355634.5_In_Frame_Del_p.HR750del|SORBS2_ENST00000319471.9_Intron	p.HR650del			O94875	SRBS2_HUMAN		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)	14	2512_2514	-		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)	650			His-rich.		A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	In_Frame_Del	DEL	ENST00000284776.7	37	c.1949_1951delACC	CCDS3845.1																																																																																				0.522	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		7	302						7	302	---	---	---	---
C6	729	broad.mit.edu	37	5	41160299	41160300	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:41160299_41160300delAC	ENST00000263413.3	-	11	1892_1893	c.1628_1629delGT	c.(1627-1629)tgtfs	p.C543fs	C6_ENST00000475349.1_5'Flank|C6_ENST00000337836.5_Frame_Shift_Del_p.C543fs	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	543	EGF-like.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGCCACTCTGACACACACACAG	0.475																																						ENST00000263413.3																			0				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96						c.(1627-1629)tfs		complement component 6																																				SO:0001589	frameshift_variant	729				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding	g.chr5:41160299_41160300delAC	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1628_1629delGT	5.37:g.41160307_41160308delAC	ENSP00000263413:p.Cys543fs					C6_ENST00000337836.5_Frame_Shift_Del_p.C543fs	p.C543fs	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN			11	1892_1893	-		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)	543			EGF-like.			Frame_Shift_Del	DEL	ENST00000263413.3	37	c.1628_1629delGT	CCDS3936.1																																																																																				0.475	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			10	854						10	854	---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130782332	130782332	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:130782332delT	ENST00000509018.1	-	22	3470	c.3265delA	c.(3265-3267)aggfs	p.R1089fs	RAPGEF6_ENST00000512052.1_Frame_Shift_Del_p.R812fs|RAPGEF6_ENST00000507093.1_Frame_Shift_Del_p.R1097fs|RAPGEF6_ENST00000296859.6_Frame_Shift_Del_p.R1097fs|CTC-432M15.3_ENST00000514667.1_Frame_Shift_Del_p.R1139fs|RAPGEF6_ENST00000307984.5_Frame_Shift_Del_p.R1102fs|RAPGEF6_ENST00000308008.6_Frame_Shift_Del_p.R1089fs	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1089					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CGGCGTGCCCTTTTTTTGTGA	0.453																																					Melanoma(168;435 1955 13113 13877 23213)	ENST00000509018.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31						c.(3265-3267)ggfs		Rap guanine nucleotide exchange factor (GEF) 6							153.0	147.0	149.0					5																	130782332		2203	4300	6503	SO:0001589	frameshift_variant	51735				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding	g.chr5:130782332delT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3265delA	5.37:g.130782332delT	ENSP00000421684:p.Arg1089fs					RAPGEF6_ENST00000308008.6_Frame_Shift_Del_p.R1089fs|FNIP1_ENST00000514667.1_Frame_Shift_Del_p.R1139fs|RAPGEF6_ENST00000512052.1_Frame_Shift_Del_p.R812fs|RAPGEF6_ENST00000507093.1_Frame_Shift_Del_p.R1097fs|RAPGEF6_ENST00000307984.5_Frame_Shift_Del_p.R1102fs|RAPGEF6_ENST00000296859.6_Frame_Shift_Del_p.R1097fs	p.R1089fs	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)	22	3470	-			1089					A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Frame_Shift_Del	DEL	ENST00000509018.1	37	c.3265delA	CCDS34225.1																																																																																				0.453	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		7	963						7	963	---	---	---	---
SLC22A4	6583	broad.mit.edu	37	5	131676327	131676327	+	Frame_Shift_Del	DEL	T	T	-	rs72552721		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:131676327delT	ENST00000200652.3	+	9	1688	c.1514delT	c.(1513-1515)cttfs	p.L505fs	AC034220.3_ENST00000437091.1_RNA|AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	505					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)	p.E509fs*1(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	ATCCTCACCCTTTTTTTCCCT	0.418																																						ENST00000200652.3																			1	Insertion - Frameshift(1)	p.E509fs*1(1)	ovary(1)	endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16						c.(1513-1515)ctfs		solute carrier family 22 (organic cation/zwitterion transporter), member 4	L-Carnitine(DB00583)						222.0	206.0	211.0					5																	131676327		2203	4300	6503	SO:0001589	frameshift_variant	6583				body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity	g.chr5:131676327delT	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1514delT	5.37:g.131676327delT	ENSP00000200652:p.Leu505fs					AC034220.3_ENST00000437091.1_RNA|AC034220.3_ENST00000417795.1_RNA	p.L505fs	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		9	1688	+		all_cancers(142;0.0752)|Breast(839;0.198)	505					O14546	Frame_Shift_Del	DEL	ENST00000200652.3	37	c.1514delT	CCDS4153.1																																																																																				0.418	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059		10	1235						10	1235	---	---	---	---
ANKHD1	54882	broad.mit.edu	37	5	139905676	139905676	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:139905676delA	ENST00000360839.2	+	26	4742	c.4588delA	c.(4588-4590)aaafs	p.K1531fs	ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.K1531fs|ANKHD1_ENST00000544120.1_5'Flank|SNORD45_ENST00000363181.1_RNA|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1531fs	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1531						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGTTTGGGAAAAAAAGGGC	0.423																																						ENST00000297183.6																			0				breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60						c.(4588-4590)aafs		ankyrin repeat and KH domain containing 1							133.0	145.0	141.0					5																	139905676		2203	4300	6503	SO:0001589	frameshift_variant	54882							g.chr5:139905676delA	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4588delA	5.37:g.139905676delA	ENSP00000354085:p.Lys1531fs					ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1531fs|ANKHD1_ENST00000360839.2_Frame_Shift_Del_p.K1531fs	p.K1531fs	NM_020690.5	NP_065741.3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		26	4712	+								A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Frame_Shift_Del	DEL	ENST00000360839.2	37	c.4588delA	CCDS4225.1																																																																																				0.423	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		11	1091						11	1091	---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168250317	168250319	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr5:168250317_168250319delTGT	ENST00000519560.1	-	7	994_996	c.575_577delACA	c.(574-579)aacatc>atc	p.N192del	SLIT3_ENST00000332966.8_In_Frame_Del_p.N192del|SLIT3_ENST00000404867.3_In_Frame_Del_p.N192del	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	192					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATGCGACTGATGTTGTTGTTGTT	0.537																																					Ovarian(29;311 847 10864 17279 24903)	ENST00000519560.1																			0				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100						c.(574-579)atc>a		slit homolog 3 (Drosophila)																																				SO:0001651	inframe_deletion	6586				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding	g.chr5:168250317_168250319delTGT	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.575_577delACA	5.37:g.168250326_168250328delTGT	ENSP00000430333:p.Asn192del					SLIT3_ENST00000404867.3_In_Frame_Del_p.NI192del|SLIT3_ENST00000332966.8_In_Frame_Del_p.NI192del	p.NI192del	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053.1	O75094	SLIT3_HUMAN	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		7	994_996	-	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	192					A6H8U9|J3KNP3|O95804|Q9UFH5	In_Frame_Del	DEL	ENST00000519560.1	37	c.575_577delACA	CCDS4369.1																																																																																				0.537	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		7	1644						7	1644	---	---	---	---
DAXX	1616	broad.mit.edu	37	6	33287898	33287900	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:33287898_33287900delTCC	ENST00000374542.5	-	5	1557_1559	c.1353_1355delGGA	c.(1351-1356)gaggaa>gaa	p.451_452EE>E	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000414083.2_In_Frame_Del_p.376_377EE>E|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_In_Frame_Del_p.451_452EE>E|ZBTB22_ENST00000418724.1_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	451	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.E451E(2)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						ctcttcttcttcctcctcctcct	0.552			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																	ENST00000374542.5				Rec	yes		6	6p21.3	1616	"""Mis, F, N"""	death-domain associated protein			E			Pancreatic neuroendocrine tumors. Paediatric GBM		2	Substitution - coding silent(2)	p.E451E(2)	prostate(1)|kidney(1)	breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						c.(1351-1356)gaa>ga		death-domain associated protein																																				SO:0001651	inframe_deletion	1616				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding	g.chr6:33287898_33287900delTCC	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1353_1355delGGA	6.37:g.33287907_33287909delTCC	ENSP00000363668:p.Glu457del					DAXX_ENST00000266000.6_In_Frame_Del_p.EE455del|DAXX_ENST00000414083.2_In_Frame_Del_p.EE380del|DAXX_ENST00000477162.1_5'UTR	p.EE455del	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN			5	1557_1559	-			455			Asp/Glu-rich (acidic).|Necessary for interaction with USP7.		B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	In_Frame_Del	DEL	ENST00000374542.5	37	c.1353_1355delGGA	CCDS4776.1																																																																																				0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			7	256						7	256	---	---	---	---
C6orf89	221477	broad.mit.edu	37	6	36867371	36867371	+	Frame_Shift_Del	DEL	C	C	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:36867371delC	ENST00000480824.2	+	3	445	c.151delC	c.(151-153)cccfs	p.P53fs	C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000373685.1_Frame_Shift_Del_p.P53fs|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.P60fs|C6orf89_ENST00000359359.2_5'UTR			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	53					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						ACCTCAGAGACCCCCCCCGCA	0.428																																						ENST00000480824.2																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						c.(151-153)ccfs		chromosome 6 open reading frame 89							62.0	69.0	66.0					6																	36867371		2203	4300	6503	SO:0001589	frameshift_variant	221477					integral to membrane		g.chr6:36867371delC	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.151delC	6.37:g.36867371delC	ENSP00000475947:p.Pro53fs					C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.P60fs|C6orf89_ENST00000373685.1_Frame_Shift_Del_p.P53fs	p.P53fs			Q6UWU4	CF089_HUMAN			3	445	+			53					B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Frame_Shift_Del	DEL	ENST00000480824.2	37	c.151delC																																																																																					0.428	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		11	399						11	399	---	---	---	---
TREML2	79865	broad.mit.edu	37	6	41168714	41168716	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:41168714_41168716delCAG	ENST00000483722.1	-	1	216_218	c.31_33delCTG	c.(31-33)ctgdel	p.L11del		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	11					T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCTGTGGCCACAGCAGCAGCAGC	0.631																																						ENST00000483722.1																			0				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18						c.(31-33)del		triggering receptor expressed on myeloid cells-like 2				143,4121		8,127,1997						4.0	1.0			26	249,8005		8,233,3886	no	coding	TREML2	NM_024807.2		16,360,5883	A1A1,A1R,RR		3.0167,3.3537,3.1315				392,12126				SO:0001651	inframe_deletion	79865				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity	g.chr6:41168714_41168716delCAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.31_33delCTG	6.37:g.41168723_41168725delCAG	ENSP00000418767:p.Leu11del						p.L11del	NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN			1	216_218	-	Ovarian(28;0.0418)|Colorectal(47;0.196)		11					Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	In_Frame_Del	DEL	ENST00000483722.1	37	c.31_33delCTG	CCDS4853.2																																																																																				0.631	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		7	189						7	189	---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42196333	42196333	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:42196333delT	ENST00000372922.4	-	18	3915	c.3353delA	c.(3352-3354)aagfs	p.K1118fs	TRERF1_ENST00000541110.1_Frame_Shift_Del_p.K1138fs|TRERF1_ENST00000372917.4_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000340840.2_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000354325.2_Frame_Shift_Del_p.K1035fs	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1118	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CTTCTGAGCCTTTTGCCTCTG	0.542																																						ENST00000541110.1																			0				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45						c.(3412-3414)agfs		transcriptional regulating factor 1							245.0	274.0	264.0					6																	42196333		2203	4300	6503	SO:0001589	frameshift_variant	55809				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding	g.chr6:42196333delT	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3353delA	6.37:g.42196333delT	ENSP00000362013:p.Lys1118fs					TRERF1_ENST00000340840.2_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000372922.4_Frame_Shift_Del_p.K1118fs|TRERF1_ENST00000372917.4_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000354325.2_Frame_Shift_Del_p.K1035fs	p.K1138fs			Q96PN7	TREF1_HUMAN	Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		18	3981	-	Colorectal(47;0.196)		1118			Interacts with CREBBP.		Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Frame_Shift_Del	DEL	ENST00000372922.4	37	c.3413delA	CCDS4867.1																																																																																				0.542	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		8	2528						8	2528	---	---	---	---
ICK	22858	broad.mit.edu	37	6	52883129	52883129	+	Splice_Site	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:52883129delT	ENST00000350082.5	-	7	1008	c.662delA	c.(661-663)aag>ag	p.K221fs	ICK_ENST00000356971.3_Splice_Site_p.K221fs	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	221	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					TATCATTACCTTTTTTGGTGT	0.502																																						ENST00000356971.3																			0				breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31						c.e8+1		intestinal cell (MAK-like) kinase							184.0	185.0	184.0					6																	52883129		2203	4300	6503	SO:0001630	splice_region_variant	22858				intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding	g.chr6:52883129delT	AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.663+1A>-	6.37:g.52883129delT						ICK_ENST00000350082.5_Splice_Site_p.K221_splice	p.K221_splice	NM_016513.4	NP_057597.2	Q9UPZ9	ICK_HUMAN			8	1151	-	Lung NSC(77;0.103)		221			Protein kinase.		A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Splice_Site	DEL	ENST00000350082.5	37	c.663_splice	CCDS4949.1																																																																																				0.502	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513	Frame_Shift_Del	10	1244						10	1244	---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	89975427	89975429	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:89975427_89975429delAAG	ENST00000402938.3	-	7	925_927	c.792_794delCTT	c.(790-795)ttcttg>ttg	p.F264del	GABRR2_ENST00000602399.1_In_Frame_Del_p.F289del	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	264					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TGTTTGGAGCAAGAAGAAGAAGA	0.517																																						ENST00000402938.3																			0				central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21						c.(790-795)ttg>tt		gamma-aminobutyric acid (GABA) A receptor, rho 2																																				SO:0001651	inframe_deletion	2570				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	g.chr6:89975427_89975429delAAG		CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4091	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 2"""	137162	"""gamma-aminobutyric acid (GABA) receptor, rho 2"""			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.792_794delCTT	6.37:g.89975436_89975438delAAG	ENSP00000386029:p.Phe264del					GABRR2_ENST00000602399.1_In_Frame_Del_p.FL289del	p.FL264del			P28476	GBRR2_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0158)	7	925_927	-		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)	289					A2BDE4|Q9H153	In_Frame_Del	DEL	ENST00000402938.3	37	c.792_794delCTT	CCDS5020.3																																																																																				0.517	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3			7	400						7	400	---	---	---	---
KIAA0408	9729	broad.mit.edu	37	6	127767596	127767596	+	Frame_Shift_Del	DEL	C	C	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:127767596delC	ENST00000483725.3	-	5	2204	c.1868delG	c.(1867-1869)ggafs	p.G623fs	SOGA3_ENST00000481848.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	623										endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		CACTTCCTGTCCCCCCCACAC	0.398																																						ENST00000483725.3																			0				endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28						c.(1867-1869)gafs		KIAA0408							236.0	227.0	230.0					6																	127767596		2203	4300	6503	SO:0001589	frameshift_variant	9729						protein binding	g.chr6:127767596delC	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1868delG	6.37:g.127767596delC	ENSP00000435150:p.Gly623fs					SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	p.G623fs	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN		GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)	5	2204	-			623					B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Frame_Shift_Del	DEL	ENST00000483725.3	37	c.1868delG	CCDS34531.1																																																																																				0.398	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		7	1720						7	1720	---	---	---	---
MED23	9439	broad.mit.edu	37	6	131919846	131919846	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:131919846delT	ENST00000368068.3	-	19	2455	c.2276delA	c.(2275-2277)aatfs	p.N759fs	MED23_ENST00000354577.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000545957.1_Frame_Shift_Del_p.N400fs|MED23_ENST00000479213.1_5'Flank|MED23_ENST00000403834.3_Frame_Shift_Del_p.N765fs|MED23_ENST00000368058.1_Frame_Shift_Del_p.N765fs|MED23_ENST00000368053.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000368060.3_Frame_Shift_Del_p.N759fs|MED23_ENST00000540546.1_Frame_Shift_Del_p.N765fs	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	759					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.N759fs*7(1)|p.N765fs*7(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		CTCCTCCACATTTTTTTTCAG	0.378																																						ENST00000403834.3																			2	Insertion - Frameshift(2)	p.N759fs*7(1)|p.N765fs*7(1)	large_intestine(2)	NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44						c.(2293-2295)atfs		mediator complex subunit 23							154.0	151.0	152.0					6																	131919846		2203	4300	6503	SO:0001589	frameshift_variant	9439				regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity	g.chr6:131919846delT	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.2276delA	6.37:g.131919846delT	ENSP00000357047:p.Asn759fs					MED23_ENST00000368058.1_Frame_Shift_Del_p.N765fs|MED23_ENST00000540546.1_Frame_Shift_Del_p.N765fs|MED23_ENST00000368053.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000368060.3_Frame_Shift_Del_p.N759fs|MED23_ENST00000354577.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000368068.3_Frame_Shift_Del_p.N759fs|MED23_ENST00000545957.1_Frame_Shift_Del_p.N400fs	p.N765fs			Q9ULK4	MED23_HUMAN		GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)	19	2467	-	Breast(56;0.0753)		759					B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Frame_Shift_Del	DEL	ENST00000368068.3	37	c.2294delA	CCDS5147.1																																																																																				0.378	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1			7	418						7	418	---	---	---	---
OLIG3	167826	broad.mit.edu	37	6	137815210	137815212	+	In_Frame_Del	DEL	TGG	TGG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:137815210_137815212delTGG	ENST00000367734.2	-	1	319_321	c.96_98delCCA	c.(94-99)caccag>cag	p.H32del		NM_175747.2	NP_786923.1	Q7RTU3	OLIG3_HUMAN	oligodendrocyte transcription factor 3	32	Poly-His.				spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron migration (GO:0097476)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.Q33K(1)		endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	11	Breast(32;0.165)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447)		ACGGCTCTCCtggtggtggtggt	0.596																																						ENST00000367734.2																			1	Substitution - Missense(1)	p.Q33K(1)	ovary(1)	endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	11						c.(94-99)cag>ca		oligodendrocyte transcription factor 3																																				SO:0001651	inframe_deletion	167826				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	g.chr6:137815210_137815212delTGG	AK096362	CCDS5186.1	6q23.3	2013-05-21			ENSG00000177468	ENSG00000177468		"""Basic helix-loop-helix proteins"""	18003	protein-coding gene	gene with protein product		609323					Standard	NM_175747		Approved	Bhlhb7, bHLHe20	uc003qhp.1	Q7RTU3	OTTHUMG00000015657	ENST00000367734.2:c.96_98delCCA	6.37:g.137815219_137815221delTGG	ENSP00000356708:p.His32del						p.HQ32del	NM_175747.2	NP_786923.1	Q7RTU3	OLIG3_HUMAN		GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447)	1	319_321	-	Breast(32;0.165)|Colorectal(23;0.24)		32			Poly-His.		Q8N8Q0	In_Frame_Del	DEL	ENST00000367734.2	37	c.96_98delCCA	CCDS5186.1																																																																																				0.596	OLIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042405.1	NM_175747		10	485						10	485	---	---	---	---
CCDC28A	25901	broad.mit.edu	37	6	139097330	139097330	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:139097330delA	ENST00000332797.6	+	2	498	c.343delA	c.(343-345)aaafs	p.K116fs		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	116								p.N117fs*5(2)		autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		TGTCAATGCCAAAAAAAATGC	0.413																																						ENST00000332797.6																			2	Deletion - Frameshift(2)	p.N117fs*5(2)	large_intestine(2)	autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13						c.(343-345)aafs		coiled-coil domain containing 28A							112.0	108.0	109.0					6																	139097330		2203	4300	6503	SO:0001589	frameshift_variant	25901							g.chr6:139097330delA	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.343delA	6.37:g.139097330delA	ENSP00000332716:p.Lys116fs						p.K116fs	NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)	2	498	+			116					E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Frame_Shift_Del	DEL	ENST00000332797.6	37	c.343delA	CCDS5192.1																																																																																				0.413	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439		10	544						10	544	---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146350671	146350672	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr6:146350671_146350672insT	ENST00000282753.1	+	1	253_254	c.18_19insT	c.(19-21)tttfs	p.F7fs	GRM1_ENST00000392299.2_Frame_Shift_Ins_p.F7fs|GRM1_ENST00000361719.2_Frame_Shift_Ins_p.F7fs|GRM1_ENST00000492807.2_Frame_Shift_Ins_p.F7fs|GRM1_ENST00000355289.4_Frame_Shift_Ins_p.F7fs|GRM1_ENST00000507907.1_Frame_Shift_Ins_p.F7fs			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	7					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GGCTCCTTTTGTTTTTTTTCCC	0.644																																						ENST00000392299.2																			0				NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126						c.(16-21)ttttttfs		glutamate receptor, metabotropic 1	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)		,	13,4249		0,13,2118					,	5.4	0.9			109	6,8248		0,6,4121	no	frameshift,frameshift	GRM1	NM_001114329.1,NM_000838.3	,	0,19,6239	A1A1,A1R,RR		0.0727,0.305,0.1518	,	,		19,12497				SO:0001589	frameshift_variant	2911				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity	g.chr6:146350671_146350672insT	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.26dupT	6.37:g.146350679_146350679dupT	ENSP00000282753:p.Phe7fs					GRM1_ENST00000355289.4_Frame_Shift_Ins_p.FF6fs|GRM1_ENST00000492807.2_Frame_Shift_Ins_p.FF6fs|GRM1_ENST00000282753.1_Frame_Shift_Ins_p.FF6fs|GRM1_ENST00000507907.1_Frame_Shift_Ins_p.FF6fs|GRM1_ENST00000361719.2_Frame_Shift_Ins_p.FF6fs	p.FF6fs			Q13255	GRM1_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	2	488_489	+		Ovarian(120;0.0387)	6					B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Frame_Shift_Ins	INS	ENST00000282753.1	37	c.18_19insT	CCDS5209.1																																																																																				0.644	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		7	1078						7	1078	---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8198250	8198251	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:8198250_8198251insT	ENST00000402384.3	-	7	877_878	c.611_612insA	c.(610-612)aacfs	p.N204fs	ICA1_ENST00000401396.1_Frame_Shift_Ins_p.N192fs|ICA1_ENST00000265577.7_Frame_Shift_Ins_p.N203fs|ICA1_ENST00000422063.2_Frame_Shift_Ins_p.N204fs|ICA1_ENST00000406470.2_Frame_Shift_Ins_p.N204fs|ICA1_ENST00000396675.3_Frame_Shift_Ins_p.N204fs|ICA1_ENST00000407906.1_Frame_Shift_Ins_p.N204fs			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	204	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)		p.N204fs*5(3)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		ATTTGTCAAAGTTTTTTTTTGC	0.376																																						ENST00000402384.3																			3	Deletion - Frameshift(3)	p.N204fs*5(3)	large_intestine(3)	breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23						c.(610-612)attfs		islet cell autoantigen 1, 69kDa																																				SO:0001589	frameshift_variant	3382				neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane		g.chr7:8198250_8198251insT		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.612dupA	7.37:g.8198259_8198259dupT	ENSP00000385570:p.Asn204fs					ICA1_ENST00000265577.7_Frame_Shift_Ins_p.I203fs|ICA1_ENST00000406470.2_Frame_Shift_Ins_p.I204fs|ICA1_ENST00000401396.1_Frame_Shift_Ins_p.I192fs|ICA1_ENST00000407906.1_Frame_Shift_Ins_p.I204fs|ICA1_ENST00000396675.3_Frame_Shift_Ins_p.I204fs|ICA1_ENST00000422063.2_Frame_Shift_Ins_p.I204fs	p.I204fs			Q05084	ICA69_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)	7	877_878	-		Ovarian(82;0.0612)	204			AH.		A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Frame_Shift_Ins	INS	ENST00000402384.3	37	c.611_612insA	CCDS34602.1																																																																																				0.376	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968		7	439						7	439	---	---	---	---
GTF2IRD2P1	401375	broad.mit.edu	37	7	72683455	72683456	+	RNA	INS	-	-	T	rs556745507	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:72683455_72683456insT	ENST00000425256.1	-	0	120									GTF2I repeat domain containing 2 pseudogene 1																		CGTTCTACCAgtttttttttgt	0.441													|||unknown(NO_COVERAGE)	44	0.00878594	0.0325	0.0014	5008	,	,		20043	0.0		0.0	False		,,,				2504	0.0					ENST00000425256.1																			0																																																			0							g.chr7:72683455_72683456insT	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72683464_72683464dupT								NR_002164.1						0	120	-									RNA	INS	ENST00000425256.1	37																																																																																						0.441	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345921.1	NR_002164		14	474						14	474	---	---	---	---
ELN	2006	broad.mit.edu	37	7	73462847	73462849	+	In_Frame_Del	DEL	GCA	GCA	-	rs140742644		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:73462847_73462849delGCA	ENST00000252034.7	+	15	1159_1161	c.760_762delGCA	c.(760-762)gcadel	p.A260del	ELN_ENST00000414324.1_In_Frame_Del_p.A255del|ELN_ENST00000380584.4_In_Frame_Del_p.A246del|ELN_ENST00000458204.1_In_Frame_Del_p.A250del|ELN_ENST00000445912.1_In_Frame_Del_p.A260del|ELN_ENST00000320492.7_In_Frame_Del_p.A224del|ELN_ENST00000380576.5_In_Frame_Del_p.A260del|ELN_ENST00000320399.6_In_Frame_Del_p.A260del|ELN_ENST00000380575.4_In_Frame_Del_p.A250del|ELN_ENST00000429192.1_In_Frame_Del_p.A265del|ELN_ENST00000357036.5_In_Frame_Del_p.A265del|ELN_ENST00000380553.4_In_Frame_Del_p.A143del|ELN_ENST00000358929.4_In_Frame_Del_p.A260del|ELN_ENST00000380562.4_In_Frame_Del_p.A260del	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	260	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				TGGCCCCCAGgcagcagcagcag	0.621			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																															ENST00000252034.7				Dom	yes		7	7q11.23	2006	T	elastin	yes	"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""	L	PAX5		B-ALL		0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32						c.(760-762)del		elastin	Rofecoxib(DB00533)																																			SO:0001651	inframe_deletion	2006				blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding	g.chr7:73462847_73462849delGCA		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.760_762delGCA	7.37:g.73462856_73462858delGCA	ENSP00000252034:p.Ala260del					ELN_ENST00000380553.4_In_Frame_Del_p.A143del|ELN_ENST00000458204.1_In_Frame_Del_p.A250del|ELN_ENST00000414324.1_In_Frame_Del_p.A255del|ELN_ENST00000429192.1_In_Frame_Del_p.A265del|ELN_ENST00000445912.1_In_Frame_Del_p.A260del|ELN_ENST00000320492.7_In_Frame_Del_p.A224del|ELN_ENST00000380562.4_In_Frame_Del_p.A260del|ELN_ENST00000357036.5_In_Frame_Del_p.A265del|ELN_ENST00000380575.4_In_Frame_Del_p.A250del|ELN_ENST00000380576.5_In_Frame_Del_p.A260del|ELN_ENST00000320399.6_In_Frame_Del_p.A260del|ELN_ENST00000380584.4_In_Frame_Del_p.A246del|ELN_ENST00000358929.4_In_Frame_Del_p.A260del	p.A260del	NM_000501.2	NP_000492.2	P15502	ELN_HUMAN			15	1159_1161	+		Lung NSC(55;0.159)	260			Ala-rich.		B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	In_Frame_Del	DEL	ENST00000252034.7	37	c.760_762delGCA	CCDS5562.2																																																																																				0.621	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		7	641						7	641	---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82595446	82595447	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:82595446_82595447insT	ENST00000333891.9	-	4	3994_3995	c.3657_3658insA	c.(3655-3660)aaactafs	p.L1220fs	PCLO_ENST00000423517.2_Frame_Shift_Ins_p.L1220fs	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCAGGGATTAGTTTTTTTTCTT	0.386																																						ENST00000423517.2																			0				breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						c.(3655-3660)aataatfs		piccolo presynaptic cytomatrix protein																																				SO:0001589	frameshift_variant	27445				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity	g.chr7:82595446_82595447insT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3658dupA	7.37:g.82595454_82595454dupT	ENSP00000334319:p.Leu1220fs					PCLO_ENST00000333891.8_Frame_Shift_Ins_p.NN1219fs	p.NN1219fs	NM_014510.2	NP_055325.2	Q9Y6V0	PCLO_HUMAN			4	3994_3995	-			1158						Frame_Shift_Ins	INS	ENST00000333891.9	37	c.3657_3658insA	CCDS47630.1																																																																																				0.386	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		8	1410						8	1410	---	---	---	---
STEAP2-AS1	100874100	broad.mit.edu	37	7	89748927	89748928	+	RNA	INS	-	-	C	rs58370593	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:89748927_89748928insC	ENST00000478318.2	-	0	424				DPY19L2P4_ENST00000497063.1_RNA|RP5-1121E10.2_ENST00000471553.1_lincRNA					STEAP2 antisense RNA 1																		GGTGCGGGCCTCCCCCTTCCCC	0.639													?|CCCCC|CCCCCC|unsure	3349	0.66873	0.7171	0.621	5008	,	,		14308	0.8095		0.5199	False		,,,				2504	0.6452					ENST00000478318.2																			0																																																			0							g.chr7:89748927_89748928insC			7q21.13	2012-10-12	2012-08-15		ENSG00000227646	ENSG00000227646		"""Long non-coding RNAs"""	40820	non-coding RNA	RNA, long non-coding			"""STEAP2 antisense RNA 1 (non-protein coding)"""				Standard	NR_110029		Approved				OTTHUMG00000065036		7.37:g.89748932_89748932dupC						DPY19L2P4_ENST00000497063.1_RNA|RP5-1121E10.2_ENST00000471553.1_lincRNA								0	424	-									RNA	INS	ENST00000478318.2	37																																																																																						0.639	STEAP2-AS1-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000350909.2			11	16						11	16	---	---	---	---
LRRC4	64101	broad.mit.edu	37	7	127670324	127670325	+	Frame_Shift_Ins	INS	-	-	G	rs368511541|rs147967619		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:127670324_127670325insG	ENST00000249363.3	-	2	626_627	c.369_370insC	c.(367-372)gccagcfs	p.S124fs	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	124					postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		GTGTTGAGGCTGGCCAGGCCGT	0.619																																						ENST00000249363.3																			0				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26						c.(367-372)gcgcctfs		leucine rich repeat containing 4																																				SO:0001589	frameshift_variant	64101					cell junction|integral to membrane|postsynaptic membrane		g.chr7:127670324_127670325insG	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"""Immunoglobulin superfamily / I-set domain containing"""	15586	protein-coding gene	gene with protein product		610486	"""leucine-rich repeat-containing 4"""			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.370dupC	7.37:g.127670326_127670326dupG	ENSP00000249363:p.Ser124fs					SND1_ENST00000354725.3_Intron	p.P124fs	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN		Lung(243;0.124)	2	626_627	-			124					A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Frame_Shift_Ins	INS	ENST00000249363.3	37	c.369_370insC	CCDS5799.1																																																																																				0.619	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		7	451						7	451	---	---	---	---
C7orf55-LUC7L2	100996928	broad.mit.edu	37	7	139094365	139094366	+	Frame_Shift_Del	DEL	AG	AG	-	rs368249579	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:139094365_139094366delAG	ENST00000354926.4	+	7	1098_1099	c.744_745delAG	c.(742-747)gaagagfs	p.EE248fs	C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs|C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs|LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AACGAAGAGAAGAGAGAGAGAG	0.391														64	0.0127796	0.028	0.0014	5008	,	,		16418	0.004		0.002	False		,,,				2504	0.0204					ENST00000354926.4																			0											c.(742-747)gaagfs						136,3410		1,134,1638						5.1	1.0			34	290,7544		0,290,3627	no	frameshift	LUC7L2	NM_016019.3		1,424,5265	A1A1,A1R,RR		3.7018,3.8353,3.7434				426,10954				SO:0001589	frameshift_variant	0							g.chr7:139094365_139094366delAG		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.744_745delAG	7.37:g.139094375_139094376delAG	ENSP00000347005:p.Glu248fs					LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs|C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs	p.EE248fs	NM_016019.3	NP_057103.2					7	1098_1099	+									Frame_Shift_Del	DEL	ENST00000354926.4	37	c.744_745delAG	CCDS43656.1																																																																																				0.391	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			8	159						8	159	---	---	---	---
TRBV7-4	28594	broad.mit.edu	37	7	142176678	142176679	+	RNA	DEL	CA	CA	-	rs147246909		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:142176678_142176679delCA	ENST00000390369.2	-	0	49									T cell receptor beta variable 7-4 (gene/pseudogene)																		GTAGTCATCGCACACACACACA	0.46																																						ENST00000390369.2																			0																	118,3528		13,92,1718						-5.4	0.0			116	306,7588		28,250,3669	no	intergenic				41,342,5387	A1A1,A1R,RR		3.8764,3.2364,3.6742				424,11116						0							g.chr7:142176678_142176679delCA	L36092		7q34	2012-02-07	2008-09-12		ENSG00000253409	ENSG00000253409		"""T cell receptors / TRB locus"""	12238	other	T cell receptor gene			"""T cell receptor beta variable 7-4"""			8650574	Standard	NG_001333		Approved	TRBV74, TCRBV6S8A2T, TCRBV7S4			OTTHUMG00000158508		7.37:g.142176688_142176689delCA														0	49	-									RNA	DEL	ENST00000390369.2	37																																																																																						0.460	TRBV7-4-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000351214.2	NG_001333		14	367						14	367	---	---	---	---
NOM1	64434	broad.mit.edu	37	7	156743209	156743211	+	In_Frame_Del	DEL	GAG	GAG	-	rs540622203	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:156743209_156743211delGAG	ENST00000275820.3	+	1	793_795	c.778_780delGAG	c.(778-780)gagdel	p.E264del		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	264	Glu-rich.|Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		ggacgaaagtgaggaggaggagg	0.552														5	0.000998403	0.0015	0.0	5008	,	,		18692	0.002		0.0	False		,,,				2504	0.001					ENST00000275820.3																			0				endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31						c.(778-780)del		nucleolar protein with MIF4G domain 1																																				SO:0001651	inframe_deletion	64434				RNA metabolic process	nucleolus	protein binding	g.chr7:156743209_156743211delGAG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.778_780delGAG	7.37:g.156743218_156743220delGAG	ENSP00000275820:p.Glu264del						p.E264del	NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)	1	793_795	+	Ovarian(565;0.218)	all_hematologic(28;0.0749)	264			Glu-rich.|Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.		Q96I08	In_Frame_Del	DEL	ENST00000275820.3	37	c.778_780delGAG	CCDS34787.1																																																																																				0.552	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		7	343						7	343	---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158704353	158704353	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr7:158704353delA	ENST00000407559.3	+	12	1731	c.1573delA	c.(1573-1575)aaafs	p.K526fs		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	526					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		AAACTTTGGGAAAAAAAATAC	0.328																																						ENST00000407559.3																			0				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35						c.(1573-1575)aafs		WD repeat domain 60																																				SO:0001589	frameshift_variant	55112							g.chr7:158704353delA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.1573delA	7.37:g.158704353delA	ENSP00000384290:p.Lys526fs						p.K526fs	NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)	12	1731	+	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	526					Q9NW58	Frame_Shift_Del	DEL	ENST00000407559.3	37	c.1573delA	CCDS47757.1																																																																																				0.328	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051		8	559						8	559	---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48701554	48701555	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:48701554_48701555insT	ENST00000314191.2	-	77	10867_10868	c.10811_10812insA	c.(10810-10812)aacfs	p.N3604fs	PRKDC_ENST00000338368.3_Frame_Shift_Ins_p.N3604fs|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	3605					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)	TTTTTTCAATGTTTTTTTTATT	0.401								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.(10810-10812)aatfs	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.chr8:48701554_48701555insT		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.10812dupA	8.37:g.48701562_48701562dupT	ENSP00000313420:p.Asn3604fs					PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Frame_Shift_Ins_p.N3604fs	p.N3604fs	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN			77	10867_10868	-		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)	3605					P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Frame_Shift_Ins	INS	ENST00000314191.2	37	c.10811_10812insA																																																																																					0.401	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		9	472						9	472	---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48746799	48746799	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:48746799delT	ENST00000314191.2	-	60	8163	c.8107delA	c.(8107-8109)aggfs	p.R2703fs	PRKDC_ENST00000338368.3_Frame_Shift_Del_p.R2703fs|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2704	KIP-binding.				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)	AGGCCCAGCCTTTTTTTCCCA	0.498								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.(8107-8109)ggfs	Non-homologous end-joining	protein kinase, DNA-activated, catalytic polypeptide							248.0	251.0	250.0					8																	48746799		1981	4176	6157	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.chr8:48746799delT		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.8107delA	8.37:g.48746799delT	ENSP00000313420:p.Arg2703fs					PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Frame_Shift_Del_p.R2703fs	p.R2703fs	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN			60	8163	-		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)	2704			KIP-binding.		P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Frame_Shift_Del	DEL	ENST00000314191.2	37	c.8107delA																																																																																					0.498	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		9	2745						9	2745	---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70514026	70514026	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:70514026delT	ENST00000260128.4	+	10	1740	c.1023delT	c.(1021-1023)cctfs	p.P341fs	SULF1_ENST00000402687.4_Frame_Shift_Del_p.P341fs|SULF1_ENST00000419716.3_Frame_Shift_Del_p.P341fs|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000458141.2_Frame_Shift_Del_p.P341fs	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	341					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TTCGTGTGCCTTTTTTTATTC	0.408																																						ENST00000260128.4																			0				breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						c.(1021-1023)ccfs		sulfatase 1							396.0	343.0	361.0					8																	70514026		2203	4300	6503	SO:0001589	frameshift_variant	23213				apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding	g.chr8:70514026delT	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.1023delT	8.37:g.70514026delT	ENSP00000260128:p.Pro341fs					SULF1_ENST00000419716.3_Frame_Shift_Del_p.P341fs|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Frame_Shift_Del_p.P341fs|SULF1_ENST00000458141.2_Frame_Shift_Del_p.P341fs	p.P341fs	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)		10	1740	+	Breast(64;0.0654)		341					Q86YV8|Q8NCA2|Q9UPS5	Frame_Shift_Del	DEL	ENST00000260128.4	37	c.1023delT	CCDS6204.1																																																																																				0.408	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		9	1693						9	1693	---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81733713	81733713	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:81733713delT	ENST00000327835.3	-	2	348	c.117delA	c.(115-117)aaafs	p.K39fs		NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	39							metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TCCGGCTGGCTTTTTTGGTGT	0.428																																						ENST00000327835.3																			0				lung(9)|skin(1)|upper_aerodigestive_tract(1)	11						c.(115-117)aafs		zinc finger protein 704							329.0	308.0	315.0					8																	81733713		2203	4300	6503	SO:0001589	frameshift_variant	619279					intracellular	zinc ion binding	g.chr8:81733713delT	AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.117delA	8.37:g.81733713delT	ENSP00000331462:p.Lys39fs						p.K39fs	NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)		2	348	-	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		39					B2RNE6|B9EGW6	Frame_Shift_Del	DEL	ENST00000327835.3	37	c.117delA	CCDS34913.1																																																																																				0.428	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2	NM_001033723		7	2491						7	2491	---	---	---	---
FTH1P11	2503	broad.mit.edu	37	8	82434138	82434138	+	RNA	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:82434138delT	ENST00000524085.2	+	0	1092				RP11-257P3.3_ENST00000523380.1_RNA|RP11-257P3.3_ENST00000518637.1_RNA																							CTGATTCACATTTTTTTCCAA	0.453																																						ENST00000523380.1																			0																																																			0							g.chr8:82434138delT																													8.37:g.82434138delT						RP11-257P3.3_ENST00000518637.1_RNA								0	200	+									RNA	DEL	ENST00000524085.2	37																																																																																						0.453	RP11-157I4.4-001	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000379364.2			7	1108						7	1108	---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103274272	103274272	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:103274272delA	ENST00000520539.1	-	55	8319	c.7713delT	c.(7711-7713)tttfs	p.F2571fs	UBR5_ENST00000220959.4_Frame_Shift_Del_p.F2570fs|UBR5_ENST00000521922.1_Frame_Shift_Del_p.F2564fs|UBR5_ENST00000518205.1_Frame_Shift_Del_p.F299fs	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2571	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTACAGGATCAAAAAAAGCAA	0.338																																					Ovarian(131;96 1741 5634 7352 27489)	ENST00000520539.1																			0				NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124						c.(7711-7713)ttfs		ubiquitin protein ligase E3 component n-recognin 5							89.0	85.0	86.0					8																	103274272		2203	4300	6503	SO:0001589	frameshift_variant	51366				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding	g.chr8:103274272delA	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.7713delT	8.37:g.103274272delA	ENSP00000429084:p.Phe2571fs					UBR5_ENST00000521922.1_Frame_Shift_Del_p.F2564fs|UBR5_ENST00000518205.1_Frame_Shift_Del_p.F299fs|UBR5_ENST00000220959.4_Frame_Shift_Del_p.F2570fs	p.F2571fs	NM_015902.5	NP_056986.2	O95071	UBR5_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;0.000442)		55	8319	-	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		2571			HECT.		B2RP24|J3KMW7|O94970|Q9NPL3	Frame_Shift_Del	DEL	ENST00000520539.1	37	c.7713delT	CCDS34933.1																																																																																				0.338	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		7	606						7	606	---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105509429	105509429	+	Frame_Shift_Del	DEL	A	A	-	rs35928649		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:105509429delA	ENST00000276654.5	-	5	1459	c.1351delT	c.(1351-1353)tgcfs	p.C451fs	LRP12_ENST00000518375.1_5'Flank|LRP12_ENST00000424843.2_Frame_Shift_Del_p.C432fs	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	451	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCTGGTTGGCAAAAAAAGCAG	0.408																																						ENST00000276654.5																			0				NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48						c.(1351-1353)gcfs		low density lipoprotein receptor-related protein 12							95.0	92.0	93.0					8																	105509429		2203	4300	6503	SO:0001589	frameshift_variant	29967				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding	g.chr8:105509429delA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1351delT	8.37:g.105509429delA	ENSP00000276654:p.Cys451fs					LRP12_ENST00000424843.2_Frame_Shift_Del_p.C432fs	p.C451fs	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)		5	1459	-			451			LDL-receptor class A 5.		A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000276654.5	37	c.1351delT	CCDS6303.1																																																																																				0.408	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		7	985						7	985	---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110455173	110455174	+	Splice_Site	INS	-	-	G	rs375659563		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr8:110455173_110455174insG	ENST00000378402.5	+	36	4497		c.e36-1			NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1						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)			ATTTTATGGCAGGTTCATTTTC	0.322										HNSCC(38;0.096)																												ENST00000378402.5																			0				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						c.e36-1		polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1																																				SO:0001630	splice_region_variant	93035				immune response	cytosol|extracellular space|integral to membrane	receptor activity	g.chr8:110455173_110455174insG	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.4394-1->G	8.37:g.110455175_110455175dupG		HNSCC(38;0.096)						NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)		36	4497	+								Q567P2|Q9UF27	Splice_Site	INS	ENST00000378402.5	37		CCDS47911.1																																																																																				0.322	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	Intron	16	680						16	680	---	---	---	---
FAM74A7	100996582	broad.mit.edu	37	9	40715923	40715924	+	lincRNA	DEL	AA	AA	-	rs374953827|rs62565543	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:40715923_40715924delAA	ENST00000432614.1	-	0	0				FAM74A3_ENST00000604146.1_lincRNA																							GAAGACGTGGAAAGAGCTCAGA	0.569																																						ENST00000604146.1																			0				endometrium(1)|large_intestine(2)|lung(6)|skin(1)	10																																														0							g.chr9:40715923_40715924delAA																													9.37:g.40715923_40715924delAA								NR_026801.1					GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)	0	262_263	+									RNA	DEL	ENST00000432614.1	37																																																																																						0.569	RP11-395E19.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143688.1			13	93						13	93	---	---	---	---
OR13C5	138799	broad.mit.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs376107801|rs201540433|rs377523807|rs199665292	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:107361451_107361452delGC	ENST00000374779.2	-	1	336_337	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGAA	0.51																																						ENST00000374779.2																			0				endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						c.(241-246)actafs		olfactory receptor, family 13, subfamily C, member 5																																				SO:0001589	frameshift_variant	138799				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr9:107361451_107361452delGC		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243_244delGC	9.37:g.107361451_107361452delGC	ENSP00000363911:p.Leu82fs						p.TL81fs	NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN			1	336_337	-			81					B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	c.243_244delGC	CCDS35091.1																																																																																				0.510	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		11	306						11	306	---	---	---	---
C9orf43	257169	broad.mit.edu	37	9	116187646	116187648	+	In_Frame_Del	DEL	GCA	GCA	-	rs374165893|rs371732185		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:116187646_116187648delGCA	ENST00000288462.4	+	10	1334_1336	c.888_890delGCA	c.(886-891)cggcag>cgg	p.Q304del	C9orf43_ENST00000374165.1_In_Frame_Del_p.Q304del	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	304	Gln-rich.									breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						agcagcagcggcagcagcagcag	0.557																																						ENST00000288462.4																			0				breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						c.(886-891)cgg>cg		chromosome 9 open reading frame 43				2,231,68,3961		0,0,0,2,0,0,231,2,64,1832						-2.8	0.0			63	18,338,431,7463		2,0,0,14,0,0,338,9,413,3349	no	codingComplex	C9orf43	NM_152786.1		2,0,0,16,0,0,569,11,477,5181	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		9.5394,7.0624,8.6957				20,569,499,11424				SO:0001651	inframe_deletion	257169							g.chr9:116187646_116187648delGCA	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.888_890delGCA	9.37:g.116187655_116187657delGCA	ENSP00000288462:p.Gln304del					C9orf43_ENST00000374165.1_In_Frame_Del_p.RQ296del	p.RQ296del	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN			10	1334_1336	+			296			Gln-rich.			In_Frame_Del	DEL	ENST00000288462.4	37	c.888_890delGCA	CCDS6796.1																																																																																				0.557	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786		12	433						12	433	---	---	---	---
GOLGA2	2801	broad.mit.edu	37	9	131019389	131019390	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:131019389_131019390insA	ENST00000421699.2	-	26	2977_2978	c.2965_2966insT	c.(2965-2967)tacfs	p.Y989fs	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Frame_Shift_Ins_p.Y977fs	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	989					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.Y977fs*9(2)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						GTCAGCCCGGTAAAAAAAAGGA	0.564																																						ENST00000421699.2																			2	Deletion - Frameshift(2)	p.Y977fs*9(2)	ovary(1)|large_intestine(1)	NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						c.(2965-2967)ccgfs		golgin A2																																				SO:0001589	frameshift_variant	2801					Golgi cisterna membrane	protein binding	g.chr9:131019389_131019390insA	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.2966dupT	9.37:g.131019397_131019397dupA	ENSP00000416097:p.Tyr989fs						p.P989fs	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN			26	2977_2978	-			989					Q6GRM9|Q9BRB0|Q9NYF9	Frame_Shift_Ins	INS	ENST00000421699.2	37	c.2965_2966insT	CCDS6896.2																																																																																				0.564	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		13	883						13	883	---	---	---	---
GTF3C5	9328	broad.mit.edu	37	9	135919216	135919216	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:135919216delT	ENST00000372097.5	+	3	798	c.475delT	c.(475-477)tttfs	p.F160fs	GTF3C5_ENST00000372108.5_Frame_Shift_Del_p.F160fs|GTF3C5_ENST00000372099.6_Frame_Shift_Del_p.F151fs|GTF3C5_ENST00000372095.5_Frame_Shift_Del_p.F35fs|GTF3C5_ENST00000342018.8_Frame_Shift_Del_p.F160fs|GTF3C5_ENST00000485692.1_3'UTR	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	160					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		GAAGGAGGCCTTTTTCCACCA	0.592																																						ENST00000372097.5																			0				endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21						c.(475-477)ttfs		general transcription factor IIIC, polypeptide 5, 63kDa							96.0	92.0	93.0					9																	135919216		2203	4300	6503	SO:0001589	frameshift_variant	9328					transcription factor TFIIIC complex	DNA binding|protein binding	g.chr9:135919216delT	AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"""General transcription factors"""	4668	protein-coding gene	gene with protein product	"""transcription factor IIIC, 63 kD"""	604890	"""general transcription factor IIIC, polypeptide 5 (63kD)"""			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.475delT	9.37:g.135919216delT	ENSP00000361169:p.Phe160fs					GTF3C5_ENST00000372108.5_Frame_Shift_Del_p.F160fs|GTF3C5_ENST00000372095.5_Frame_Shift_Del_p.F35fs|GTF3C5_ENST00000485692.1_3'UTR|GTF3C5_ENST00000342018.8_Frame_Shift_Del_p.F160fs|GTF3C5_ENST00000372099.6_Frame_Shift_Del_p.F151fs	p.F160fs	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)	3	798	+			160					A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Frame_Shift_Del	DEL	ENST00000372097.5	37	c.475delT	CCDS6958.1																																																																																				0.592	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		7	727						7	727	---	---	---	---
TUBBP5	643224	broad.mit.edu	37	9	141069809	141069809	+	RNA	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr9:141069809delT	ENST00000503395.1	+	0	1023									tubulin, beta pseudogene 5																		CTCCCGTCTCTTGCAGTTCTG	0.662																																						ENST00000503395.1																			0																																																			0							g.chr9:141069809delT	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141069809delT														0	1023	+									RNA	DEL	ENST00000503395.1	37																																																																																						0.662	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156		5	10						5	10	---	---	---	---
SYT15	83849	broad.mit.edu	37	10	46969401	46969403	+	In_Frame_Del	DEL	CAG	CAG	-	rs368995487		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:46969401_46969403delCAG	ENST00000374321.4	-	2	124_126	c.58_60delCTG	c.(58-60)ctgdel	p.L21del	SYT15_ENST00000374323.4_Intron|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374325.3_In_Frame_Del_p.L21del|SYT15_ENST00000503753.1_In_Frame_Del_p.L21del	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CCCCGATCAACAGCAGCAGCAGC	0.631																																					Ovarian(57;1152 1428 19651 37745)	ENST00000374325.3																			0				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						c.(58-60)del		synaptotagmin XV																																				SO:0001651	inframe_deletion	83849					integral to membrane|plasma membrane		g.chr10:46969401_46969403delCAG	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.58_60delCTG	10.37:g.46969410_46969412delCAG	ENSP00000363441:p.Leu21del					SYT15_ENST00000374321.4_In_Frame_Del_p.L21del|SYT15_ENST00000503753.1_In_Frame_Del_p.L21del|SYT15_ENST00000374323.3_Intron	p.L21del	NM_181519.2	NP_852660.1	Q9BQS2	SYT15_HUMAN			2	210_212	-			21					A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	In_Frame_Del	DEL	ENST00000374321.4	37	c.58_60delCTG	CCDS44376.1																																																																																				0.631	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		7	335						7	335	---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88753099	88753100	+	RNA	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:88753099_88753100insT	ENST00000444431.1	+	0	64				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										AATGAGTTTACTTTTTTTTTTA	0.307																																						ENST00000444431.1																			0													ankyrin repeat and GTPase domain Arf GTPase activating protein 11																																						119385				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding	g.chr10:88753099_88753100insT			10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88753109_88753109dupT						RP11-96C23.5_ENST00000433214.2_RNA				Q8TF27	AGA11_HUMAN			0	64	+								B9EIP7|D3DWE4	RNA	INS	ENST00000444431.1	37																																																																																						0.307	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		11	226						11	226	---	---	---	---
HECTD2	143279	broad.mit.edu	37	10	93247481	93247481	+	Frame_Shift_Del	DEL	A	A	-	rs57105282		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:93247481delA	ENST00000298068.5	+	11	1231	c.1137delA	c.(1135-1137)gcafs	p.A379fs	HECTD2_ENST00000498446.1_3'UTR|HECTD2_ENST00000536715.1_Intron|HECTD2_ENST00000446394.1_Frame_Shift_Del_p.A383fs|HECTD2_ENST00000371667.1_Frame_Shift_Del_p.A29fs	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	379					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CTGTAGCTGCAAAAAAAATCA	0.318																																					NSCLC(12;376 469 1699 39910 41417)	ENST00000446394.1																			0				breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						c.(1147-1149)gcfs		HECT domain containing E3 ubiquitin protein ligase 2							93.0	97.0	96.0					10																	93247481		2203	4297	6500	SO:0001589	frameshift_variant	143279				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity	g.chr10:93247481delA	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.1137delA	10.37:g.93247481delA	ENSP00000298068:p.Ala379fs					HECTD2_ENST00000298068.5_Frame_Shift_Del_p.A379fs|HECTD2_ENST00000536715.1_Intron|HECTD2_ENST00000498446.1_3'UTR|HECTD2_ENST00000371667.1_Frame_Shift_Del_p.A29fs	p.A383fs			Q5U5R9	HECD2_HUMAN			12	1249	+			379					Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Frame_Shift_Del	DEL	ENST00000298068.5	37	c.1149delA	CCDS7414.1																																																																																				0.318	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			7	729						7	729	---	---	---	---
C10orf82	143379	broad.mit.edu	37	10	118424338	118424338	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:118424338delT	ENST00000369210.3	-	4	449	c.395delA	c.(394-396)aacfs	p.N132fs	C10orf82_ENST00000588184.1_Frame_Shift_Del_p.N132fs	NM_144661.2	NP_653262.1	Q8WW14	CJ082_HUMAN	chromosome 10 open reading frame 82	132										endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7				all cancers(201;0.0143)		CTTGTAGCAGTTTTTGGCCAT	0.567																																						ENST00000369210.3																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						c.(394-396)acfs		chromosome 10 open reading frame 82							158.0	140.0	146.0					10																	118424338		2203	4300	6503	SO:0001589	frameshift_variant	143379							g.chr10:118424338delT	BC021737	CCDS7596.1	10q26.12	2012-05-31			ENSG00000165863	ENSG00000165863			28500	protein-coding gene	gene with protein product						12477932	Standard	NM_144661		Approved	MGC33547, Em:AC016825.4	uc001lcr.3	Q8WW14	OTTHUMG00000019105	ENST00000369210.3:c.395delA	10.37:g.118424338delT	ENSP00000358212:p.Asn132fs					C10orf82_ENST00000588184.1_Frame_Shift_Del_p.N132fs	p.N132fs	NM_144661.2	NP_653262.1	Q8WW14	CJ082_HUMAN		all cancers(201;0.0143)	4	449	-			132					B3KUM9|D3DRC3	Frame_Shift_Del	DEL	ENST00000369210.3	37	c.395delA	CCDS7596.1																																																																																				0.567	C10orf82-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000050527.1	NM_144661		7	914						7	914	---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129902204	129902205	+	Frame_Shift_Del	DEL	TG	TG	-	rs143354291		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr10:129902204_129902205delTG	ENST00000368654.3	-	13	8274_8275	c.7899_7900delCA	c.(7897-7902)cacaaafs	p.HK2633fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.HK2273fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2633	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GCTGGTTCTTTGTGTGTGTGTG	0.5																																						ENST00000368654.3																			0				NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159						c.(7897-7902)caaafs		marker of proliferation Ki-67																																				SO:0001589	frameshift_variant	4288				cell proliferation	nucleolus	ATP binding|protein C-terminus binding	g.chr10:129902204_129902205delTG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.7899_7900delCA	10.37:g.129902214_129902215delTG	ENSP00000357643:p.His2633fs					MKI67_ENST00000368653.3_Frame_Shift_Del_p.HK2273fs	p.HK2633fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN			13	8274_8275	-		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)	2633			16 X 122 AA approximate repeats.		Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	37	c.7899_7900delCA	CCDS7659.1																																																																																				0.500	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		20	655						20	655	---	---	---	---
MUC15	143662	broad.mit.edu	37	11	26587426	26587427	+	5'UTR	INS	-	-	T	rs201956622		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:26587426_26587427insT	ENST00000455601.2	-	0	97_98				ANO3_ENST00000531568.1_Intron|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000281268.8_Frame_Shift_Ins_p.P21fs|MUC15_ENST00000529533.1_Frame_Shift_Ins_p.P21fs|MUC15_ENST00000436318.2_Frame_Shift_Ins_p.P21fs|MUC15_ENST00000527569.1_Frame_Shift_Ins_p.P21fs|ANO3_ENST00000256737.3_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						TTTGGTATTGGTTTTTTTTTAA	0.287																																						ENST00000436318.2																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						c.(58-63)aacaatfs		mucin 15, cell surface associated																																				SO:0001623	5_prime_UTR_variant	143662					extracellular region|integral to membrane|plasma membrane		g.chr11:26587426_26587427insT	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"""Mucins"""	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.-22->A	11.37:g.26587435_26587435dupT						MUC15_ENST00000455601.2_5'UTR|MUC15_ENST00000527569.1_Frame_Shift_Ins_p.NN20fs|MUC15_ENST00000529533.1_Frame_Shift_Ins_p.NN20fs|ANO3_ENST00000537978.1_Intron|MUC15_ENST00000281268.8_Frame_Shift_Ins_p.NN20fs|ANO3_ENST00000531568.1_Intron|ANO3_ENST00000256737.3_Intron|ANO3_ENST00000525139.1_Intron	p.NN20fs			Q8N387	MUC15_HUMAN			2	193_194	-			0					B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Frame_Shift_Ins	INS	ENST00000455601.2	37	c.60_61insA	CCDS7859.1																																																																																				0.287	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		9	273						9	273	---	---	---	---
OR4C46	119749	broad.mit.edu	37	11	51515689	51515690	+	Frame_Shift_Del	DEL	GT	GT	-	rs536939786		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:51515689_51515690delGT	ENST00000328188.1	+	1	408_409	c.408_409delGT	c.(406-411)cagtgtfs	p.C137fs		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCATGAACCAGTGTGTGTGTGC	0.48																																						ENST00000328188.1																			0				endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						c.(406-411)cagtfs		olfactory receptor, family 4, subfamily C, member 46																																				SO:0001589	frameshift_variant	119749				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:51515689_51515690delGT		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.408_409delGT	11.37:g.51515697_51515698delGT	ENSP00000329056:p.Cys137fs						p.QC136fs	NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN			1	408_409	+			136						Frame_Shift_Del	DEL	ENST00000328188.1	37	c.408_409delGT	CCDS31498.1																																																																																				0.480	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		7	1025						7	1025	---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63525788	63525788	+	3'UTR	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:63525788delT	ENST00000377819.5	+	0	3368				RTN3_ENST00000354497.4_Frame_Shift_Del_p.A190fs|RTN3_ENST00000537981.1_3'UTR|RTN3_ENST00000356000.3_3'UTR|C11orf95_ENST00000433688.1_lincRNA|RTN3_ENST00000339997.4_3'UTR|RTN3_ENST00000540798.1_3'UTR|RTN3_ENST00000341307.2_3'UTR	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3						apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						CATTCCAAGCTTTTTTTTTAA	0.348																																						ENST00000354497.4																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						c.(568-570)gcfs		reticulon 3							48.0	49.0	49.0					11																	63525788		2201	4298	6499	SO:0001624	3_prime_UTR_variant	10313				apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane		g.chr11:63525788delT	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.*115T>-	11.37:g.63525788delT						RTN3_ENST00000356000.3_3'UTR|RTN3_ENST00000341307.2_3'UTR|RTN3_ENST00000339997.4_3'UTR|RTN3_ENST00000537981.1_3'UTR|RTN3_ENST00000377819.5_3'UTR|RTN3_ENST00000540798.1_3'UTR	p.A190fs	NM_001265591.1	NP_001252520.1	O95197	RTN3_HUMAN			4	634	+			0					B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Frame_Shift_Del	DEL	ENST00000377819.5	37	c.570delT	CCDS58141.1																																																																																				0.348	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		10	281						10	281	---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	67018079	67018081	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:67018079_67018081delGAG	ENST00000529006.2	+	17	3024_3026	c.2578_2580delGAG	c.(2578-2580)gagdel	p.E866del	KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_In_Frame_Del_p.E427del|KDM2A_ENST00000398645.2_Intron|KDM2A_ENST00000308783.5_In_Frame_Del_p.E324del	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	866					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						ggaggaggaagaggaggaggagg	0.655																																						ENST00000529006.2																			0				NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						c.(2578-2580)del		lysine (K)-specific demethylase 2A																																				SO:0001651	inframe_deletion	22992				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding	g.chr11:67018079_67018081delGAG	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2578_2580delGAG	11.37:g.67018088_67018090delGAG	ENSP00000432786:p.Glu866del					KDM2A_ENST00000398645.2_Intron|KDM2A_ENST00000308783.5_In_Frame_Del_p.E324del|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_In_Frame_Del_p.E427del	p.E866del	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN			17	3024_3026	+			866					D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	In_Frame_Del	DEL	ENST00000529006.2	37	c.2578_2580delGAG	CCDS44657.1																																																																																				0.655	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308		7	219						7	219	---	---	---	---
ATG16L2	89849	broad.mit.edu	37	11	72528863	72528865	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:72528863_72528865delAGG	ENST00000321297.5	+	3	419_421	c.281_283delAGG	c.(280-285)caggag>cag	p.E98del	ATG16L2_ENST00000534905.1_In_Frame_Del_p.E98del	NM_033388.1	NP_203746.1	Q8NAA4	A16L2_HUMAN	autophagy related 16-like 2 (S. cerevisiae)	98					autophagy (GO:0006914)|negative stranded viral RNA replication (GO:0039689)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	14			BRCA - Breast invasive adenocarcinoma(5;2.73e-06)			GTGAAGTGGCAGGAGGAGGAGGA	0.591																																						ENST00000321297.5																			0				breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	14						c.(280-285)cag>c		autophagy related 16-like 2 (S. cerevisiae)																																				SO:0001651	inframe_deletion	89849				autophagy|protein transport	cytoplasm	protein binding	g.chr11:72528863_72528865delAGG	AK024423	CCDS31634.1	11q13.4	2014-02-12	2012-06-06		ENSG00000168010	ENSG00000168010		"""WD repeat domain containing"""	25464	protein-coding gene	gene with protein product			"""ATG16 autophagy related 16-like 2 (S. cerevisiae)"""			11214971	Standard	XM_005274378		Approved	FLJ00012, WDR80, ATG16B	uc001otd.3	Q8NAA4	OTTHUMG00000167961	ENST00000321297.5:c.281_283delAGG	11.37:g.72528872_72528874delAGG	ENSP00000326340:p.Glu98del					ATG16L2_ENST00000534905.1_In_Frame_Del_p.QE94del	p.QE94del	NM_033388.1	NP_203746.1	Q8NAA4	A16L2_HUMAN	BRCA - Breast invasive adenocarcinoma(5;2.73e-06)		3	419_421	+			94					A5PL30|B2RPK5|Q658V4|Q6PID3|Q8NBG0	In_Frame_Del	DEL	ENST00000321297.5	37	c.281_283delAGG	CCDS31634.1																																																																																				0.591	ATG16L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397305.1	NM_033388		7	288						7	288	---	---	---	---
POLD3	10714	broad.mit.edu	37	11	74336609	74336609	+	Frame_Shift_Del	DEL	A	A	-	rs375954131		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:74336609delA	ENST00000263681.2	+	8	1019	c.890delA	c.(889-891)gaafs	p.E297fs	POLD3_ENST00000532497.1_Frame_Shift_Del_p.E191fs|POLD3_ENST00000527458.1_Frame_Shift_Del_p.E258fs	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	297					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CTGCAGAAGGAAAAAAAAAGG	0.458																																						ENST00000263681.2																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18						c.(889-891)gafs		polymerase (DNA-directed), delta 3, accessory subunit							27.0	29.0	29.0					11																	74336609		2198	4291	6489	SO:0001589	frameshift_variant	10714				base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding	g.chr11:74336609delA	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.890delA	11.37:g.74336609delA	ENSP00000263681:p.Glu297fs					POLD3_ENST00000527458.1_Frame_Shift_Del_p.E258fs|POLD3_ENST00000532497.1_Frame_Shift_Del_p.E191fs	p.E297fs	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN			8	1019	+	Breast(11;3.21e-06)		297					B7ZAI6|Q32MZ9|Q32N00	Frame_Shift_Del	DEL	ENST00000263681.2	37	c.890delA	CCDS8233.1																																																																																				0.458	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591		9	254						9	254	---	---	---	---
TSKU	25987	broad.mit.edu	37	11	76506673	76506675	+	In_Frame_Del	DEL	CTG	CTG	-	rs149062181		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:76506673_76506675delCTG	ENST00000527881.1	+	2	1039_1041	c.13_15delCTG	c.(13-15)ctgdel	p.L9del	TSKU_ENST00000333090.4_In_Frame_Del_p.L9del			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	9					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					GCCGTGGCCCCTGCTGCTGCTGC	0.616																																						ENST00000527881.1																			0				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12						c.(13-15)del		tsukushi, small leucine rich proteoglycan																																				SO:0001651	inframe_deletion	25987					extracellular region		g.chr11:76506673_76506675delCTG	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.13_15delCTG	11.37:g.76506682_76506684delCTG	ENSP00000434847:p.Leu9del					TSKU_ENST00000333090.4_In_Frame_Del_p.L9del	p.L9del			Q8WUA8	TSK_HUMAN			2	1039_1041	+	Ovarian(111;0.112)		9					B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	In_Frame_Del	DEL	ENST00000527881.1	37	c.13_15delCTG	CCDS8246.1																																																																																				0.616	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		20	425						20	425	---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89106662	89106663	+	Splice_Site	INS	-	-	A	rs548576417|rs552289081|rs56022003	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:89106662_89106663insA	ENST00000263317.4	-	12	1313		c.e12-2		NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000535633.1_Splice_Site|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000343727.5_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000375979.3_Splice_Site|NOX4_ENST00000534731.1_Splice_Site|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000532825.1_Splice_Site			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4						bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.?(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				AGTTGGACACTAAAAAAAAATA	0.292													?|AAAAAAAAA|AAAAAAAAAA|unsure	31	0.0061901	0.0227	0.0014	5008	,	,		14064	0.0		0.0	False		,,,				2504	0.0					ENST00000535633.1																			1	Unknown(1)	p.?(1)	ovary(1)	NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44						c.e12-2		NADPH oxidase 4			,,	92,4164		2,88,2038					,,	5.2	1.0		dbSNP_129	80	7,8213		0,7,4103	no	splice-3,splice-3,splice-3	NOX4	NM_016931.3,NM_001143837.1,NM_001143836.1	,,	2,95,6141	A1A1,A1R,RR		0.0852,2.1617,0.7935	,,	,,		99,12377				SO:0001630	splice_region_variant	50507				cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity	g.chr11:89106662_89106663insA	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1075-2->T	11.37:g.89106671_89106671dupA						NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000532825.1_Splice_Site|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000263317.4_Splice_Site|NOX4_ENST00000375979.3_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000534731.1_Splice_Site|NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000343727.5_Splice_Site		NM_001143836.1|NM_016931.3	NP_001137308.1|NP_058627.1	Q9NPH5	NOX4_HUMAN			12	1313	-		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)						A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Splice_Site	INS	ENST00000263317.4	37		CCDS8285.1																																																																																				0.292	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	Intron	10	934						10	934	---	---	---	---
KDM4D	55693	broad.mit.edu	37	11	94730806	94730807	+	Frame_Shift_Ins	INS	-	-	A	rs142280183		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr11:94730806_94730807insA	ENST00000335080.5	+	3	1102_1103	c.270_271insA	c.(271-273)aaafs	p.K91fs	KDM4D_ENST00000536741.1_Frame_Shift_Ins_p.K91fs	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	91	Poly-Lys.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTCAATACCATAAAAAAAAGAA	0.455																																						ENST00000335080.5																			0				endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						c.(268-273)caaaaafs		lysine (K)-specific demethylase 4D																																				SO:0001589	frameshift_variant	55693				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr11:94730806_94730807insA	AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"""Chromatin-modifying enzymes / K-demethylases"""	25498	protein-coding gene	gene with protein product		609766	"""jumonji domain containing 2D"""	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.278dupA	11.37:g.94730814_94730814dupA	ENSP00000334181:p.Lys91fs					KDM4D_ENST00000536741.1_Frame_Shift_Ins_p.QK90fs	p.QK90fs	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN			3	1102_1103	+			90					B3KPC4|Q0VF39|Q9NT41|Q9NW76	Frame_Shift_Ins	INS	ENST00000335080.5	37	c.270_271insA	CCDS8302.1																																																																																				0.455	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039		9	862						9	862	---	---	---	---
RECQL	5965	broad.mit.edu	37	12	21644546	21644547	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:21644546_21644547insT	ENST00000444129.2	-	3	588_589	c.120_121insA	c.(118-123)aaagtcfs	p.V41fs	RECQL_ENST00000421138.2_Frame_Shift_Ins_p.V41fs	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	41					DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.V41fs*2(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TTTGTCAGGACTTTTTTTTTCT	0.381								Other identified genes with known or suspected DNA repair function																														ENST00000444129.2																			1	Deletion - Frameshift(1)	p.V41fs*2(1)	large_intestine(1)	endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						c.(118-123)aatcctfs	Other identified genes with known or suspected DNA repair function	RecQ protein-like (DNA helicase Q1-like)			,	10,4254		0,10,2122					,	3.3	0.2			53	10,8244		0,10,4117	no	frameshift,frameshift	RECQL	NM_032941.2,NM_002907.3	,	0,20,6239	A1A1,A1R,RR		0.1212,0.2345,0.1598	,	,		20,12498				SO:0001589	frameshift_variant	5965				DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding	g.chr12:21644546_21644547insT	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"""DNA helicase Q1-like"""	600537	"""RecQ protein-like (DNA helicase Q1-like)"""			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.121dupA	12.37:g.21644555_21644555dupT	ENSP00000416739:p.Val41fs					RECQL_ENST00000421138.2_Frame_Shift_Ins_p.NP40fs	p.NP40fs	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN			3	588_589	-			40					A8K6G2	Frame_Shift_Ins	INS	ENST00000444129.2	37	c.120_121insA	CCDS31756.1																																																																																				0.381	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		13	742						13	742	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26640046	26640046	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:26640046delT	ENST00000381340.3	-	40	5925	c.5509delA	c.(5509-5511)aggfs	p.R1837fs		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1837					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TCATCGTCCCTTTTTTTGTTA	0.358																																						ENST00000381340.3																		ETV6/ITPR2(2)	0				biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125						c.(5509-5511)ggfs		inositol 1,4,5-trisphosphate receptor, type 2							206.0	188.0	193.0					12																	26640046		1860	4102	5962	SO:0001589	frameshift_variant	3709				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity	g.chr12:26640046delT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5509delA	12.37:g.26640046delT	ENSP00000370744:p.Arg1837fs						p.R1837fs	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN			40	5925	-	Colorectal(261;0.0847)		1837					O94773	Frame_Shift_Del	DEL	ENST00000381340.3	37	c.5509delA	CCDS41764.1																																																																																				0.358	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		8	1249						8	1249	---	---	---	---
OVCH1	341350	broad.mit.edu	37	12	29596301	29596301	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:29596301delT	ENST00000318184.5	-	25	3149	c.3150delA	c.(3148-3150)aaafs	p.K1050fs	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	1050						extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TACCTATTAATTTTTTTCCTG	0.348																																						ENST00000318184.5																			0				NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92						c.(3148-3150)aafs		ovochymase 1							122.0	122.0	122.0					12																	29596301		1820	4078	5898	SO:0001589	frameshift_variant	341350				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity	g.chr12:29596301delT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.3150delA	12.37:g.29596301delT	ENSP00000326708:p.Lys1050fs					OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	p.K1050fs	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN			25	3149	-	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)		1050						Frame_Shift_Del	DEL	ENST00000318184.5	37	c.3150delA																																																																																					0.348	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		11	1346						11	1346	---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49087434	49087436	+	In_Frame_Del	DEL	ATG	ATG	-	rs371197465		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:49087434_49087436delATG	ENST00000261900.3	-	9	1783_1785	c.1561_1563delCAT	c.(1561-1563)catdel	p.H521del		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	521	His-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AGTGGTGATTATGATGATGATGA	0.443																																						ENST00000261900.3																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						c.(1561-1563)del		cyclin T1				12,4250		0,12,2119						4.8	1.0			307	3,8241		1,1,4120	no	coding	CCNT1	NM_001240.2		1,13,6239	A1A1,A1R,RR		0.0364,0.2816,0.1199				15,12491				SO:0001651	inframe_deletion	904				cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding	g.chr12:49087434_49087436delATG	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1561_1563delCAT	12.37:g.49087443_49087445delATG	ENSP00000261900:p.His521del						p.H521del	NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN			9	1783_1785	-			521			His-rich.		A9XU13|E7EX76|O60581	In_Frame_Del	DEL	ENST00000261900.3	37	c.1561_1563delCAT	CCDS8766.1																																																																																				0.443	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		7	2118						7	2118	---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64491019	64491019	+	Splice_Site	DEL	A	A	-	rs79989081		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:64491019delA	ENST00000355086.3	+	15	2202		c.e15-1		SRGAP1_ENST00000357825.3_Splice_Site|RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000543397.1_Splice_Site	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.?(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTTTTTTTTTAGGTGAAAATC	0.348																																						ENST00000355086.3																			1	Unknown(1)	p.?(1)	central_nervous_system(1)	breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65						c.e15-1		SLIT-ROBO Rho GTPase activating protein 1							43.0	45.0	44.0					12																	64491019		2203	4300	6503	SO:0001630	splice_region_variant	57522				axon guidance	cytosol		g.chr12:64491019delA	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1679-1A>-	12.37:g.64491019delA						RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000357825.3_Splice_Site|SRGAP1_ENST00000543397.1_Splice_Site		NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)	15	2202	+								Q9H8A3|Q9P2P2	Splice_Site	DEL	ENST00000355086.3	37		CCDS8967.1																																																																																				0.348	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		Intron	9	277						9	277	---	---	---	---
TMEM19	55266	broad.mit.edu	37	12	72094757	72094757	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr12:72094757delT	ENST00000266673.5	+	6	1587	c.993delT	c.(991-993)ggtfs	p.G331fs		NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	331						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		CTGCTTGGGGTTTTTGGCCCA	0.433																																						ENST00000266673.5																			0				large_intestine(1)|lung(8)	9						c.(991-993)ggfs		transmembrane protein 19							199.0	184.0	189.0					12																	72094757		2203	4300	6503	SO:0001589	frameshift_variant	55266					integral to membrane		g.chr12:72094757delT	BC008596	CCDS9002.1	12q15	2004-03-04				ENSG00000139291			25605	protein-coding gene	gene with protein product						12477932	Standard	NM_018279		Approved	FLJ10936	uc001sws.3	Q96HH6	OTTHUMG00000169558	ENST00000266673.5:c.993delT	12.37:g.72094757delT	ENSP00000266673:p.Gly331fs						p.G331fs	NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN		GBM - Glioblastoma multiforme(134;0.044)	6	1587	+		Breast(359;0.0889)	331					B2RDL2|Q53FY3|Q9NV41	Frame_Shift_Del	DEL	ENST00000266673.5	37	c.993delT	CCDS9002.1																																																																																				0.433	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279		7	998						7	998	---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	20041394	20041394	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr13:20041394delA	ENST00000400230.2	-	7	527	c.483delT	c.(481-483)tttfs	p.F161fs	TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.F161fs|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382978.1_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	161					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTTAATGTCAAAAAAAATGT	0.303																																						ENST00000400230.2																			0				NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(481-483)ttfs		transmembrane phosphoinositide 3-phosphatase and tensin homolog 2			,,	4,21,4229		0,0,4,1,19,2103	46.0	51.0	49.0		,,	2.4	0.0	13		49	5,25,8188		0,1,4,4,16,4084	no	codingComplex,intron,intron	TPTE2	NM_199254.2,NM_130785.3,NM_001141968.1	,,	0,1,8,5,35,6187	A1A1,A1A2,A1R,A2A2,A2R,RR		0.3651,0.5877,0.441	,,	,,	20041394	9,46,12417	2200	4283	6483	SO:0001589	frameshift_variant	93492					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr13:20041394delA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.483delT	13.37:g.20041394delA	ENSP00000383089:p.Phe161fs					TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.F161fs|TPTE2_ENST00000382978.1_Intron|TPTE2_ENST00000390680.2_Intron	p.F161fs			Q6XPS3	TPTE2_HUMAN		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)	7	527	-		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)	161					A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Frame_Shift_Del	DEL	ENST00000400230.2	37	c.483delT	CCDS45014.1																																																																																				0.303	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		7	385						7	385	---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25527490	25527491	+	RNA	INS	-	-	AAAAAG	rs375560921|rs201773491	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr13:25527490_25527491insAAAAAG	ENST00000429698.1	-	0	282							Q5T6R2	TPT2L_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 1																		AGGAAGGTTCTAAAAAAAATTT	0.252														9	0.00179712	0.0008	0.0014	5008	,	,		20326	0.004		0.003	False		,,,				2504	0.0					ENST00000429698.1																			0																																																			0							g.chr13:25527490_25527491insAAAAAG			13q12.12-q12.13	2012-10-03			ENSG00000253771	ENSG00000253771			35196	pseudogene	pseudogene							Standard	NR_026730		Approved		uc010tdh.2	Q5T6R2	OTTHUMG00000016596		13.37:g.25527490_25527491insAAAAAG														0	282	-								B3KST4|B4DMH9	RNA	INS	ENST00000429698.1	37																																																																																						0.252	TPTE2P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000044206.1			10	45						10	45	---	---	---	---
EEF1DP3	196549	broad.mit.edu	37	13	32527507	32527508	+	RNA	DEL	GT	GT	-	rs369428918		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr13:32527507_32527508delGT	ENST00000428783.1	+	0	1207_1208							Q658K8	EF1DL_HUMAN	eukaryotic translation elongation factor 1 delta pseudogene 3								translation elongation factor activity (GO:0003746)										TCTGGCCTGAGTGTGTGTGTGT	0.46																																						ENST00000428783.1																			0																																																			0							g.chr13:32527507_32527508delGT			13q13.1	2012-10-23			ENSG00000229715	ENSG00000229715			30486	pseudogene	pseudogene						12477932	Standard	NR_027062		Approved		uc001utu.3	Q658K8	OTTHUMG00000016691		13.37:g.32527517_32527518delGT														0	1207_1208	+								Q08AR3	RNA	DEL	ENST00000428783.1	37																																																																																						0.460	EEF1DP3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000044400.2	NR_027062		11	283						11	283	---	---	---	---
TRAV9-2	28677	broad.mit.edu	37	14	22409533	22409539	+	RNA	DEL	CTCTCTC	CTCTCTC	-	rs374912343|rs371270332|rs2178778|rs587678559|rs201742006|rs367992314	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:22409533_22409539delCTCTCTC	ENST00000390441.2	+	0	102									T cell receptor alpha variable 9-2																		ctctctctctctctctctTTTTTTTTT	0.415																																						ENST00000390441.2																			0																																																			0							g.chr14:22409533_22409539delCTCTCTC	AE000659		14q11.2	2012-02-07			ENSG00000211793	ENSG00000211793		"""T cell receptors / TRA locus"""	12154	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000170637		14.37:g.22409533_22409539delCTCTCTC														0	102	+									RNA	DEL	ENST00000390441.2	37																																																																																						0.415	TRAV9-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409885.1	NG_001332		8	36						8	36	---	---	---	---
TRAV12-3	28672	broad.mit.edu	37	14	22433684	22433684	+	RNA	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:22433684delT	ENST00000390442.3	+	0	5									T cell receptor alpha variable 12-3																		TTTGTTATTATTTTTTTTTCG	0.353																																						ENST00000390442.3																			0																	15,18,3471		0,0,15,3,12,1722	101.0	91.0	94.0			-7.1	0.0	14		93	12,36,7756		0,0,12,5,26,3859	no	intergenic				0,0,27,8,38,5581	A1A1,A1A2,A1R,A2A2,A2R,RR		0.6151,0.9418,0.7163			22433684	27,54,11227	692	1591	2283			0							g.chr14:22433684delT	X06193		14q11.2	2012-02-07			ENSG00000211794	ENSG00000211794		"""T cell receptors / TRA locus"""	12107	other	T cell receptor gene						3501368, 8951372	Standard	NG_001332		Approved	TRAV123, TCRAV2S2, TCRAV12S3			OTTHUMG00000170640		14.37:g.22433684delT														0	5	+									RNA	DEL	ENST00000390442.3	37																																																																																						0.353	TRAV12-3-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409888.1	NG_001332		7	219						7	219	---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35592700	35592700	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:35592700delT	ENST00000557565.1	+	2	630	c.249delT	c.(247-249)catfs	p.H83fs	KIAA0391_ENST00000534898.4_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000603588.1_Intron|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000603544.1_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000321130.10_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000604948.1_Intron|PPP2R3C_ENST00000261475.5_5'Flank	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	83					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		CTGTTCCTCATTTTTTTTTAG	0.423																																						ENST00000557565.1																			0				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14						c.(247-249)cafs		KIAA0391							49.0	48.0	48.0					14																	35592700		2203	4300	6503	SO:0001589	frameshift_variant	9692				tRNA processing	mitochondrion		g.chr14:35592700delT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 3"", ""proteinaceous RNase P"""	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.249delT	14.37:g.35592700delT	ENSP00000454657:p.His83fs					KIAA0391_ENST00000534898.4_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000603544.1_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000321130.10_Frame_Shift_Del_p.H83fs	p.H83fs			O15091	MRRP3_HUMAN	Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)	2	630	+	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		83					B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Frame_Shift_Del	DEL	ENST00000557565.1	37	c.249delT	CCDS32063.1																																																																																				0.423	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		7	383						7	383	---	---	---	---
FBXO33	254170	broad.mit.edu	37	14	39871612	39871612	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:39871612delT	ENST00000298097.7	-	2	1040	c.703delA	c.(703-705)attfs	p.I235fs	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	235					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		TACTGTTTAATTTTTTTGCCA	0.323																																						ENST00000298097.7																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9						c.(703-705)ttfs		F-box protein 33							102.0	94.0	97.0					14																	39871612		2203	4300	6503	SO:0001589	frameshift_variant	254170							g.chr14:39871612delT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.703delA	14.37:g.39871612delT	ENSP00000298097:p.Ile235fs					FBXO33_ENST00000554190.1_Intron	p.I235fs	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)	2	1040	-	Hepatocellular(127;0.213)		235					Q6PIR2|Q86TR2|Q86YE0	Frame_Shift_Del	DEL	ENST00000298097.7	37	c.703delA	CCDS9677.1																																																																																				0.323	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			7	362						7	362	---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73572607	73572608	+	Frame_Shift_Del	DEL	AG	AG	-	rs150988201		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:73572607_73572608delAG	ENST00000261973.7	+	11	1480_1481	c.1195_1196delAG	c.(1195-1197)agafs	p.R399fs	RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	399	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		agagcgggaaagagagagagag	0.446																																						ENST00000261973.7																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31						c.(1195-1197)afs		RNA binding motif protein 25																																				SO:0001589	frameshift_variant	58517				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding	g.chr14:73572607_73572608delAG	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1195_1196delAG	14.37:g.73572617_73572618delAG	ENSP00000261973:p.Arg399fs					RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	11	1480_1481	+			399			Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.		A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Frame_Shift_Del	DEL	ENST00000261973.7	37	c.1195_1196delAG	CCDS32113.1																																																																																				0.446	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		10	200						10	200	---	---	---	---
GLRX5	51218	broad.mit.edu	37	14	95999677	95999677	+	5'Flank	DEL	A	A	-	rs373834979		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:95999677delA	ENST00000331334.4	+	0	0				SNHG10_ENST00000553559.1_RNA|SCARNA13_ENST00000516672.1_RNA|SNHG10_ENST00000555866.1_RNA|SNHG10_ENST00000554169.1_RNA|SNHG10_ENST00000500370.2_RNA	NM_016417.2	NP_057501.2	Q86SX6	GLRX5_HUMAN	glutaredoxin 5						cell redox homeostasis (GO:0045454)|hemopoiesis (GO:0030097)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|protein disulfide oxidoreductase activity (GO:0015035)			large_intestine(1)|lung(1)	2		all_cancers(154;0.135)		Epithelial(152;0.133)|COAD - Colon adenocarcinoma(157;0.21)|all cancers(159;0.212)		CTCAAAGTTTAAAAAAAAAAA	0.353																																						ENST00000500370.2																			0																	25,19,1892		7,0,11,3,13,934	118.0	126.0	124.0			-1.1	0.0	14		126	13,57,4076		4,0,5,2,53,2009	no	near-gene-5				11,0,16,5,66,2943	A1A1,A1A2,A1R,A2A2,A2R,RR		1.6884,2.2727,1.8744			95999677	38,76,5968	876	1991	2867	SO:0001631	upstream_gene_variant	0							g.chr14:95999677delA	AF113691	CCDS9936.1	14q32.2	2007-08-16	2007-08-16	2005-11-11		ENSG00000182512			20134	protein-coding gene	gene with protein product		609588	"""chromosome 14 open reading frame 87"", ""glutaredoxin 5 homolog (S. cerevisiae)"""	C14orf87			Standard	NM_016417		Approved	PR01238, GRX5	uc001yem.1	Q86SX6			14.37:g.95999677delA	Exception_encountered					SNHG10_ENST00000554169.1_RNA|SNHG10_ENST00000553559.1_RNA|SNHG10_ENST00000555866.1_RNA								0	766	-								Q0X088|Q3YML0|Q86WY3|Q8IZ54	RNA	DEL	ENST00000331334.4	37		CCDS9936.1																																																																																				0.353	GLRX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414550.1			51	623						51	623	---	---	---	---
IGHV3-43	28426	broad.mit.edu	37	14	106926652	106926653	+	RNA	DEL	TC	TC	-	rs142878466|rs372523377		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr14:106926652_106926653delTC	ENST00000434710.1	-	0	71_72									immunoglobulin heavy variable 3-43																		CATGGTGCGTTCTCTGTGTTCA	0.495																																						ENST00000434710.1																			0																	1556,2152		51,1454,349						-3.6	0.2		dbSNP_134	145	2136,5764		153,1830,1967	no	intergenic				204,3284,2316	A1A1,A1R,RR		27.038,41.9633,31.8057				3692,7916						0							g.chr14:106926652_106926653delTC	M99672		14q32.33	2012-02-08			ENSG00000232216	ENSG00000232216		"""Immunoglobulins / IGH locus"""	5604	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152094		14.37:g.106926654_106926655delTC														0	71_72	-									RNA	DEL	ENST00000434710.1	37																																																																																						0.495	IGHV3-43-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325191.1	NG_001019		20	1055						20	1055	---	---	---	---
GOLGA8DP	100132979	broad.mit.edu	37	15	22709778	22709779	+	RNA	DEL	TC	TC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:22709778_22709779delTC	ENST00000314246.8	-	0	1069				RN7SL545P_ENST00000495815.2_RNA			Q0D2H9	GOG8D_HUMAN	golgin A8 family, member D, pseudogene							Golgi apparatus (GO:0005794)											CATGCTACCATCTCTCTCTCTG	0.535																																						ENST00000314246.8																			0																																																			0							g.chr15:22709778_22709779delTC			15q11.2	2014-04-10	2011-04-15	2010-02-12	ENSG00000185182	ENSG00000185182			32376	pseudogene	pseudogene			"""golgi autoantigen, golgin subfamily a, 8D"""	GOLGA8D		12477932	Standard	NR_027407		Approved		uc010axw.2	Q0D2H9	OTTHUMG00000171882		15.37:g.22709786_22709787delTC														0	1069	-									RNA	DEL	ENST00000314246.8	37																																																																																						0.535	GOLGA8DP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415613.1	NR_027407		7	1015						7	1015	---	---	---	---
FAN1	22909	broad.mit.edu	37	15	31196894	31196894	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:31196894delA	ENST00000362065.4	+	2	319	c.28delA	c.(28-30)aaafs	p.K11fs	FAN1_ENST00000561594.1_Frame_Shift_Del_p.K11fs|FAN1_ENST00000565466.1_Frame_Shift_Del_p.K11fs|FAN1_ENST00000561607.1_Frame_Shift_Del_p.K11fs	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	11					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						ACCTCCTGACAAAAAAAGGCC	0.353								Direct reversal of damage																														ENST00000362065.4																			0				autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						c.(28-30)aafs	Direct reversal of damage	FANCD2/FANCI-associated nuclease 1							77.0	87.0	84.0					15																	31196894		2202	4300	6502	SO:0001589	frameshift_variant	22909				double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding	g.chr15:31196894delA		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.28delA	15.37:g.31196894delA	ENSP00000354497:p.Lys11fs					FAN1_ENST00000561607.1_Frame_Shift_Del_p.K11fs|FAN1_ENST00000565466.1_Frame_Shift_Del_p.K11fs|FAN1_ENST00000561594.1_Frame_Shift_Del_p.K11fs	p.K11fs	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN			2	319	+			11					A8K4M2|Q86WU8	Frame_Shift_Del	DEL	ENST00000362065.4	37	c.28delA	CCDS32186.1																																																																																				0.353	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		7	775						7	775	---	---	---	---
SRP14	6727	broad.mit.edu	37	15	40328597	40328599	+	In_Frame_Del	DEL	TGC	TGC	-	rs371085676|rs377432895	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:40328597_40328599delTGC	ENST00000267884.6	-	5	417_419	c.346_348delGCA	c.(346-348)gcadel	p.A116del	SRP14_ENST00000558527.1_5'UTR|SRP14_ENST00000560773.1_In_Frame_Del_p.A36del|SRP14-AS1_ENST00000504245.1_lincRNA|SRP14_ENST00000558720.1_In_Frame_Del_p.A36del	NM_003134.4	NP_003125.3	P37108	SRP14_HUMAN	signal recognition particle 14kDa (homologous Alu RNA binding protein)	116	Ala/Thr-rich.				cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercellular bridge (GO:0045171)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|skin(1)|upper_aerodigestive_tract(1)	3		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)		ctgcggcaggtgctgctgctgct	0.478																																						ENST00000267884.6																			0				endometrium(1)|skin(1)|upper_aerodigestive_tract(1)	3						c.(346-348)del		signal recognition particle 14kDa (homologous Alu RNA binding protein)																																				SO:0001651	inframe_deletion	6727				negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding	g.chr15:40328597_40328599delTGC		CCDS42017.1	15q22	2008-08-15	2002-08-29		ENSG00000140319	ENSG00000140319			11299	protein-coding gene	gene with protein product		600708	"""signal recognition particle 14kD (homologous Alu RNA-binding protein)"""			8196634	Standard	NM_003134		Approved	ALURBP, MGC14326	uc001zkq.2	P37108		ENST00000267884.6:c.346_348delGCA	15.37:g.40328606_40328608delTGC	ENSP00000267884:p.Ala116del					SRP14_ENST00000560773.1_In_Frame_Del_p.A36del|SRP14_ENST00000558720.1_In_Frame_Del_p.A36del|SRP14_ENST00000558527.1_5'UTR	p.A116del	NM_003134.4	NP_003125.3	P37108	SRP14_HUMAN		GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)	5	417_419	-		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)	116			Ala/Thr-rich.		B5BUF5|Q6B0K5|Q96Q14	In_Frame_Del	DEL	ENST00000267884.6	37	c.346_348delGCA	CCDS42017.1																																																																																				0.478	SRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418262.2	NM_003134		7	419						7	419	---	---	---	---
SECISBP2L	9728	broad.mit.edu	37	15	49304896	49304896	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:49304896delT	ENST00000559471.1	-	12	1943	c.1680delA	c.(1678-1680)aaafs	p.K560fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.K515fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	560							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TCTCTTTTCCTTTTTTTGCTT	0.333																																						ENST00000559471.1																			0				breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						c.(1678-1680)aafs		SECIS binding protein 2-like							106.0	111.0	109.0					15																	49304896		2197	4295	6492	SO:0001589	frameshift_variant	9728							g.chr15:49304896delT	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1680delA	15.37:g.49304896delT	ENSP00000453854:p.Lys560fs					SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.K515fs	p.K560fs	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN			12	1943	-			560					Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	37	c.1680delA	CCDS53942.1																																																																																				0.333	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		7	715						7	715	---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59182564	59182565	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr15:59182564_59182565delCT	ENST00000380516.2	-	15	2081_2082	c.1994_1995delAG	c.(1993-1995)gagfs	p.E665fs	SLTM_ENST00000536328.1_Frame_Shift_Del_p.E234fs|AC025918.2_ENST00000452467.1_RNA	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	665	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TTTCTAGGCGCTCTCTCTCTCT	0.475																																						ENST00000380516.2																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(1993-1995)gfs		SAFB-like, transcription modulator																																				SO:0001589	frameshift_variant	79811				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding	g.chr15:59182564_59182565delCT	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.1994_1995delAG	15.37:g.59182574_59182575delCT	ENSP00000369887:p.Glu665fs					AC025918.2_ENST00000452467.1_RNA|SLTM_ENST00000536328.1_Frame_Shift_Del_p.E234fs	p.E665fs	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN			15	2081_2082	-			665			Arg/Glu-rich.		A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Frame_Shift_Del	DEL	ENST00000380516.2	37	c.1994_1995delAG	CCDS10168.2																																																																																				0.475	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		26	898						26	898	---	---	---	---
RP11-420N3.2	0	broad.mit.edu	37	16	5313074	5313076	+	RNA	DEL	GGT	GGT	-	rs542176654		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:5313074_5313076delGGT	ENST00000569895.1	+	0	304				AC074051.1_ENST00000408882.1_RNA																							GCAGggtgacggtggtggtggtg	0.483																																						ENST00000569895.1																			0																																																			0							g.chr16:5313074_5313076delGGT																													16.37:g.5313083_5313085delGGT														0	304	+									RNA	DEL	ENST00000569895.1	37																																																																																						0.483	RP11-420N3.2-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000435404.2			15	285						15	285	---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28931200	28931202	+	In_Frame_Del	DEL	CTG	CTG	-	rs373504496		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:28931200_28931202delCTG	ENST00000358201.4	-	3	925_927	c.337_339delCAG	c.(337-339)cagdel	p.Q113del	RABEP2_ENST00000561803.1_5'UTR|RABEP2_ENST00000357573.6_In_Frame_Del_p.Q113del|RABEP2_ENST00000544477.1_In_Frame_Del_p.Q42del	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	113	Poly-Gln.				endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						CCTCACAGTCCTGCTGCTGCTGC	0.64																																					Pancreas(66;639 1284 10093 31061 49099)	ENST00000358201.4																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						c.(337-339)del		rabaptin, RAB GTPase binding effector protein 2																																				SO:0001651	inframe_deletion	79874				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity	g.chr16:28931200_28931202delCTG	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.337_339delCAG	16.37:g.28931209_28931211delCTG	ENSP00000350934:p.Gln113del					RABEP2_ENST00000561803.1_5'UTR|RABEP2_ENST00000357573.6_In_Frame_Del_p.Q113del|RABEP2_ENST00000544477.1_In_Frame_Del_p.Q42del	p.Q113del	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN			3	925_927	-			113			Poly-Gln.			In_Frame_Del	DEL	ENST00000358201.4	37	c.337_339delCAG	CCDS42140.1																																																																																				0.640	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		10	372						10	372	---	---	---	---
RP11-19N8.4	0	broad.mit.edu	37	16	33070154	33070154	+	lincRNA	DEL	C	C	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:33070154delC	ENST00000561541.1	-	0	291																											CCTATCACATCCCATTCCAGC	0.488																																						ENST00000561541.1																			0																																																			0							g.chr16:33070154delC																													16.37:g.33070154delC														0	291	-									RNA	DEL	ENST00000561541.1	37																																																																																						0.488	RP11-19N8.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000432096.1			12	36						12	36	---	---	---	---
RP11-23E10.4	0	broad.mit.edu	37	16	33365420	33365420	+	RNA	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:33365420delA	ENST00000568520.1	-	0	249																											TACAAACTATAAAAAAACAGA	0.358																																						ENST00000568520.1																			0																																																			0							g.chr16:33365420delA																													16.37:g.33365420delA														0	249	-									RNA	DEL	ENST00000568520.1	37																																																																																						0.358	RP11-23E10.4-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432134.1			9	72						9	72	---	---	---	---
RP11-51O6.1	0	broad.mit.edu	37	16	61089294	61089308	+	RNA	DEL	TTCTTCTTCTTTTTT	TTCTTCTTCTTTTTT	-	rs567241949|rs184755071|rs56076856|rs371501468|rs61593494|rs542919512|rs201948984|rs78942570|rs200517879|rs572952892	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:61089294_61089308delTTCTTCTTCTTTTTT	ENST00000591758.1	-	0	560_566																											GGTTGATAGCttcttcttctttttttttttttttt	0.237																																						ENST00000591758.1																			0																																																			0							g.chr16:61089294_61089308delTTCTTCTTCTTTTTT																													16.37:g.61089294_61089308delTTCTTCTTCTTTTTT														0	560_566	-									RNA	DEL	ENST00000591758.1	37																																																																																						0.237	RP11-51O6.1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000460612.1			24	102						24	102	---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72822564	72822566	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:72822564_72822566delTGC	ENST00000268489.5	-	10	10281_10283	c.9609_9611delGCA	c.(9607-9612)cagcaa>caa	p.3203_3204QQ>Q	RP5-991G20.4_ENST00000569195.1_RNA|RP5-991G20.1_ENST00000563328.2_RNA|AC004943.1_ENST00000584072.1_RNA|ZFHX3_ENST00000397992.5_In_Frame_Del_p.2289_2290QQ>Q	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3203	Poly-Gln.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cacctgtggttgctgctgctgct	0.65																																						ENST00000268489.5																			0				NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153						c.(9607-9612)caa>ca		zinc finger homeobox 3																																				SO:0001651	inframe_deletion	463				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr16:72822564_72822566delTGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.9609_9611delGCA	16.37:g.72822573_72822575delTGC	ENSP00000268489:p.Gln3204del					ZFHX3_ENST00000397992.5_In_Frame_Del_p.QQ2289del	p.QQ3203del	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN			10	10281_10283	-		Ovarian(137;0.13)	3203			Poly-Gln.		D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	c.9609_9611delGCA	CCDS10908.1																																																																																				0.650	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		11	780						11	780	---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77334227	77334228	+	Frame_Shift_Ins	INS	-	-	G	rs148849944		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:77334227_77334228insG	ENST00000282849.5	-	17	3024_3025	c.2606_2607insC	c.(2605-2607)ccafs	p.P869fs		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	869	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TTTTTGTGGCTGGTGGAGTTCC	0.46																																						ENST00000282849.5																			0				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						c.(2605-2607)cgcfs		ADAM metallopeptidase with thrombospondin type 1 motif, 18																																				SO:0001589	frameshift_variant	170692				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr16:77334227_77334228insG	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2607dupC	16.37:g.77334229_77334229dupG	ENSP00000282849:p.Pro869fs						p.R869fs	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN			17	3024_3025	-			869			Spacer.		Q6P4R5|Q6ZWJ9	Frame_Shift_Ins	INS	ENST00000282849.5	37	c.2606_2607insC	CCDS10926.1																																																																																				0.460	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			7	549						7	549	---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89349640	89349641	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr16:89349640_89349641insT	ENST00000301030.4	-	9	3769_3770	c.3309_3310insA	c.(3307-3312)aaagatfs	p.D1104fs	ANKRD11_ENST00000378330.2_Frame_Shift_Ins_p.D1104fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1104	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TTCTTGTCATCTTTTTTTTCAG	0.465																																						ENST00000301030.4																			0				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83						c.(3307-3312)aaatgafs		ankyrin repeat domain 11																																				SO:0001589	frameshift_variant	29123					nucleus		g.chr16:89349640_89349641insT	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3310dupA	16.37:g.89349648_89349648dupT	ENSP00000301030:p.Asp1104fs					ANKRD11_ENST00000378330.2_Frame_Shift_Ins_p.*1104fs	p.*1104fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)	9	3769_3770	-		all_hematologic(23;0.00824)|Colorectal(91;0.0475)	1104			Lys-rich.		Q6NTG1|Q6QMF8	Frame_Shift_Ins	INS	ENST00000301030.4	37	c.3309_3310insA	CCDS32513.1																																																																																				0.465	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		18	1014						18	1014	---	---	---	---
TP53	7157	broad.mit.edu	37	17	7579518	7579519	+	Frame_Shift_Ins	INS	-	-	TT	rs574255227	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr17:7579518_7579519insTT	ENST00000269305.4	-	4	357_358	c.168_169insAA	c.(166-171)gaagacfs	p.D57fs	TP53_ENST00000455263.2_Frame_Shift_Ins_p.D57fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.D57fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Ins_p.D57fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.D57fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.D57fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	57	Interaction with HRMT1L2.				apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.A63fs*66(3)|p.E51fs*59(1)|p.E56E(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)|p.D57fs*86(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGACCTGGGTCTTCAGTGAACC	0.599		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	ENST00000420246.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		18	Whole gene deletion(8)|Deletion - Frameshift(5)|Insertion - Frameshift(3)|Substitution - coding silent(1)|Deletion - In frame(1)	p.0?(8)|p.A63fs*66(3)|p.E51fs*59(1)|p.E56E(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)|p.D57fs*86(1)	liver(4)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(2)|upper_aerodigestive_tract(1)|stomach(1)|breast(1)|prostate(1)|pancreas(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185						c.(166-171)gaacccfs	Other conserved DNA damage response genes	tumor protein p53																																				SO:0001589	frameshift_variant	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7579518_7579519insTT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.167_168dupAA	17.37:g.7579519_7579520dupTT	ENSP00000269305:p.Asp57fs	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_ENST00000413465.2_Frame_Shift_Ins_p.P57fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.P57fs|TP53_ENST00000269305.4_Frame_Shift_Ins_p.P57fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.P57fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.P57fs	p.P57fs	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	4	300_301	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	57			Interaction with HRMT1L2.		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	c.168_169insAA	CCDS11118.1																																																																																				0.599	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		553	615						553	615	---	---	---	---
RP11-178C3.1	0	broad.mit.edu	37	17	58050859	58050859	+	IGR	DEL	C	C	-	rs368813643		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr17:58050859delC	ENST00000591035.1	+	0	481				RP11-178C3.2_ENST00000586209.1_lincRNA																							TTTTTTTTGGCAGTTTTTACT	0.418																																						ENST00000586209.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr17:58050859delC																													17.37:g.58050859delC														0	158	+									RNA	DEL	ENST00000591035.1	37																																																																																						0.418	RP11-178C3.1-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000449157.1			10	92						10	92	---	---	---	---
ROCK1P1	727758	broad.mit.edu	37	18	112519	112520	+	RNA	INS	-	-	A	rs199734221		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr18:112519_112520insA	ENST00000608049.1	+	0	389					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		CCAGCTCCCCCGGGGCCTCCGT	0.53																																						ENST00000576266.1																			0																																																			0							g.chr18:112519_112520insA			18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.112519_112520insA														0	153_154	+									RNA	INS	ENST00000608049.1	37																																																																																						0.530	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			7	90						7	90	---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21750331	21750331	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr18:21750331delT	ENST00000319481.3	-	24	2584	c.2378delA	c.(2377-2379)aatfs	p.N793fs	OSBPL1A_ENST00000357041.4_Frame_Shift_Del_p.N411fs|OSBPL1A_ENST00000399443.3_Frame_Shift_Del_p.N280fs|RNA5SP452_ENST00000363004.1_RNA	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	793					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TTTCTTATCATTTTTTTTGTA	0.393																																						ENST00000319481.3																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36						c.(2377-2379)atfs		oxysterol binding protein-like 1A							259.0	233.0	242.0					18																	21750331		2203	4300	6503	SO:0001589	frameshift_variant	114876				cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding	g.chr18:21750331delT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.2378delA	18.37:g.21750331delT	ENSP00000320291:p.Asn793fs					OSBPL1A_ENST00000399443.3_Frame_Shift_Del_p.N280fs|OSBPL1A_ENST00000357041.4_Frame_Shift_Del_p.N411fs	p.N793fs	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN			24	2584	-	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)		793					B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Del	DEL	ENST00000319481.3	37	c.2378delA	CCDS11884.1																																																																																				0.393	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		7	892						7	892	---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48593481	48593482	+	Frame_Shift_Ins	INS	-	-	T			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr18:48593481_48593482insT	ENST00000342988.3	+	10	1770_1771	c.1232_1233insT	c.(1231-1236)agttacfs	p.Y412fs	SMAD4_ENST00000398417.2_Frame_Shift_Ins_p.Y412fs|SMAD4_ENST00000588745.1_Frame_Shift_Ins_p.Y316fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	412	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TTTGTACAGAGTTACTACTTAG	0.426																																						ENST00000342988.3																			38	Whole gene deletion(36)|Unknown(2)	p.0?(36)|p.?(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454						c.(1231-1233)atafs		SMAD family member 4																																				SO:0001589	frameshift_variant	4089				BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	g.chr18:48593481_48593482insT	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1234dupT	18.37:g.48593483_48593483dupT	ENSP00000341551:p.Tyr412fs					SMAD4_ENST00000398417.2_Frame_Shift_Ins_p.I411fs|SMAD4_ENST00000588745.1_Frame_Shift_Ins_p.I315fs	p.I411fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)	10	1770_1771	+		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)	411			MH2.		A8K405	Frame_Shift_Ins	INS	ENST00000342988.3	37	c.1232_1233insT	CCDS11950.1																																																																																				0.426	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		109	223						109	223	---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7585352	7585353	+	In_Frame_Ins	INS	-	-	GCT	rs552712605	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:7585352_7585353insGCT	ENST00000597229.1	+	2	1394_1395	c.1224_1225insGCT	c.(1225-1227)gct>GCTgct	p.409_409A>AA	CTD-2207O23.11_ENST00000602083.1_RNA|ZNF358_ENST00000394341.2_In_Frame_Ins_p.409_409A>AA|MCOLN1_ENST00000264079.6_5'Flank	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	409	Poly-Ala.				embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						ctgccgcggccgctgcagctgc	0.703																																						ENST00000597229.1																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						c.(1222-1227)gcctgc>gcGCTctgc		zinc finger protein 358																																				SO:0001652	inframe_insertion	140467				embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:7585352_7585353insGCT	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1225_1227dupGCT	19.37:g.7585353_7585355dupGCT	ENSP00000472305:p.Ala416dup					ZNF358_ENST00000394341.2_In_Frame_Ins_p.408_409AC>ALC	p.408_409AC>ALC	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN			2	1394_1395	+			408			Poly-Ala.		Q9BTM7	In_Frame_Ins	INS	ENST00000597229.1	37	c.1224_1225insGCT	CCDS32890.2																																																																																				0.703	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1			10	45						10	45	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9063127	9063128	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:9063127_9063128insA	ENST00000397910.4	-	3	24521_24522	c.24318_24319insT	c.(24316-24321)tttgagfs	p.E8107fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8109	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGCTAGTCTCAAAAAAGCCAG	0.495																																						ENST00000397910.4																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(24316-24321)ttagacfs		mucin 16, cell surface associated																																				SO:0001589	frameshift_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9063127_9063128insA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.24319dupT	19.37:g.9063133_9063133dupA	ENSP00000381008:p.Glu8107fs						p.LD8106fs	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN			3	24521_24522	-			8108			Ser-rich.|Thr-rich.		Q6ZQW5|Q96RK2	Frame_Shift_Ins	INS	ENST00000397910.4	37	c.24318_24319insT	CCDS54212.1																																																																																				0.495	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		244	432						244	432	---	---	---	---
ZNF44	51710	broad.mit.edu	37	19	12384448	12384448	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:12384448delA	ENST00000356109.5	-	5	884	c.766delT	c.(766-768)tggfs	p.W256fs	ZNF44_ENST00000355684.5_Frame_Shift_Del_p.W208fs	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	256					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AAACTGGGCCAAAAAAAGGCT	0.398																																						ENST00000356109.5																			0				ovary(1)	1						c.(766-768)ggfs		zinc finger protein 44							88.0	93.0	92.0					19																	12384448		2203	4300	6503	SO:0001589	frameshift_variant	51710				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding	g.chr19:12384448delA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.766delT	19.37:g.12384448delA	ENSP00000348419:p.Trp256fs					ZNF44_ENST00000355684.5_Frame_Shift_Del_p.W208fs	p.W256fs	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)	5	884	-		Renal(1328;0.157)	256					B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Frame_Shift_Del	DEL	ENST00000356109.5	37	c.766delT	CCDS54223.1																																																																																				0.398	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		9	811						9	811	---	---	---	---
ZNF443	10224	broad.mit.edu	37	19	12542364	12542364	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:12542364delA	ENST00000301547.5	-	4	819	c.622delT	c.(622-624)tggfs	p.W208fs	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	208					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						AAACTGGGCCAAAAAAACGCT	0.408																																						ENST00000301547.5																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						c.(622-624)ggfs		zinc finger protein 443							98.0	99.0	98.0					19																	12542364		2203	4299	6502	SO:0001589	frameshift_variant	10224				induction of apoptosis|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:12542364delA	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.622delT	19.37:g.12542364delA	ENSP00000301547:p.Trp208fs					CTD-3105H18.16_ENST00000595562.1_Intron	p.W208fs	NM_005815.4	NP_005806.2	Q9Y2A4	ZN443_HUMAN			4	819	-			208						Frame_Shift_Del	DEL	ENST00000301547.5	37	c.622delT	CCDS32918.1																																																																																				0.408	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		7	1059						7	1059	---	---	---	---
SLC7A9	11136	broad.mit.edu	37	19	33353391	33353393	+	In_Frame_Del	DEL	TGA	TGA	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:33353391_33353393delTGA	ENST00000023064.4	-	5	769_771	c.578_580delTCA	c.(577-582)atcagc>agc	p.I193del	SLC7A9_ENST00000590341.1_In_Frame_Del_p.I193del|SLC7A9_ENST00000587772.1_In_Frame_Del_p.I193del|RN7SKP22_ENST00000365097.1_RNA	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	193			I -> II (in CSNU). {ECO:0000269|PubMed:11157794}.		amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	ACCAGCCCGCTGATGATGATGAT	0.631																																					GBM(181;1335 2108 9644 44178 46689)	ENST00000023064.4																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32						c.(577-582)agc>a		solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	L-Cystine(DB00138)																																			SO:0001651	inframe_deletion	11136				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding	g.chr19:33353391_33353393delTGA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.578_580delTCA	19.37:g.33353400_33353402delTGA	ENSP00000023064:p.Ile193del					SLC7A9_ENST00000587772.1_In_Frame_Del_p.IS193del|SLC7A9_ENST00000590341.1_In_Frame_Del_p.IS193del	p.IS193del	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN			5	769_771	-	Esophageal squamous(110;0.137)		193		I -> II (in CSNU).			B2R9A6	In_Frame_Del	DEL	ENST00000023064.4	37	c.578_580delTCA	CCDS12425.1																																																																																				0.631	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			7	521						7	521	---	---	---	---
FAM98C	147965	broad.mit.edu	37	19	38899502	38899504	+	In_Frame_Del	DEL	AAG	AAG	-	rs372349446		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:38899502_38899504delAAG	ENST00000252530.5	+	8	1049_1051	c.1030_1032delAAG	c.(1030-1032)aagdel	p.K349del	FAM98C_ENST00000588262.1_3'UTR|FAM98C_ENST00000343358.7_In_Frame_Del_p.K267del	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	349										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TTGGGGTCGCAAGAAGAAGAAGA	0.606																																						ENST00000252530.5																			0				endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15						c.(1030-1032)del		family with sequence similarity 98, member C				414,186,2888		21,2,370,1,182,1168						-2.6	0.1		dbSNP_134	37	186,506,7042		7,0,172,3,500,3185	no	codingComplex	FAM98C	NM_174905.3		28,2,542,4,682,4353	A1A1,A1A2,A1R,A2A2,A2R,RR		8.9475,17.2018,11.5131				600,692,9930				SO:0001651	inframe_deletion	147965							g.chr19:38899502_38899504delAAG		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.1030_1032delAAG	19.37:g.38899511_38899513delAAG	ENSP00000252530:p.Lys349del					FAM98C_ENST00000343358.7_In_Frame_Del_p.K267del|FAM98C_ENST00000588262.1_3'UTR	p.K349del	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		8	1049_1051	+	all_cancers(60;3.95e-06)		349					A6NMW3|Q66K45	In_Frame_Del	DEL	ENST00000252530.5	37	c.1030_1032delAAG	CCDS42562.1																																																																																				0.606	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		27	543						27	543	---	---	---	---
LIPE-AS1	100996307	broad.mit.edu	37	19	43136362	43136363	+	RNA	DEL	TG	TG	-	rs142080128		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:43136362_43136363delTG	ENST00000594688.1	+	0	1450				LIPE-AS1_ENST00000594624.2_RNA	NR_073179.1				LIPE antisense RNA 1																		TGAGTATGTATGTGTGTGTGTG	0.505																																						ENST00000594688.1																			0																																																			0							g.chr19:43136362_43136363delTG	AK096849, BM974950		19q13.2	2013-05-21			ENSG00000213904	ENSG00000213904		"""Long non-coding RNAs"""	48589	non-coding RNA	RNA, long non-coding							Standard	NR_073179		Approved				OTTHUMG00000182815		19.37:g.43136372_43136373delTG						LIPE-AS1_ENST00000594624.2_RNA		NR_073179.1						0	1450	+									RNA	DEL	ENST00000594688.1	37																																																																																						0.505	LIPE-AS1-004	KNOWN	basic	antisense	antisense	OTTHUMT00000464099.1	NR_073179		11	194						11	194	---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47935681	47935683	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:47935681_47935683delTCC	ENST00000236877.6	-	9	2525_2527	c.2130_2132delGGA	c.(2128-2133)gaggac>gac	p.E710del	SLC8A2_ENST00000539381.1_In_Frame_Del_p.E173del|SLC8A2_ENST00000542837.1_In_Frame_Del_p.E466del|SLC8A2_ENST00000601757.1_5'UTR	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	710					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		CCGGGACCCGTCCTCCTCCTCCT	0.616																																						ENST00000236877.6																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31						c.(2128-2133)gac>ga		solute carrier family 8 (sodium/calcium exchanger), member 2																																				SO:0001651	inframe_deletion	6543				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding	g.chr19:47935681_47935683delTCC	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"""Solute carriers"""	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.2130_2132delGGA	19.37:g.47935690_47935692delTCC	ENSP00000236877:p.Glu710del					SLC8A2_ENST00000542837.1_In_Frame_Del_p.ED466del|SLC8A2_ENST00000539381.1_In_Frame_Del_p.ED173del|SLC8A2_ENST00000601757.1_5'UTR	p.ED710del	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)	9	2525_2527	-		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)	710					B4DYQ9	In_Frame_Del	DEL	ENST00000236877.6	37	c.2130_2132delGGA	CCDS33065.1																																																																																				0.616	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			12	762						12	762	---	---	---	---
FUZ	80199	broad.mit.edu	37	19	50310483	50310485	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:50310483_50310485delCAG	ENST00000313777.4	-	11	1343_1345	c.1180_1182delCTG	c.(1180-1182)ctgdel	p.L394del	AC006942.4_ENST00000600669.1_RNA|FUZ_ENST00000533418.1_In_Frame_Del_p.L344del|FUZ_ENST00000528094.1_In_Frame_Del_p.L358del|FUZ_ENST00000445575.2_Intron	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN	fuzzy planar cell polarity protein	394	Leu-rich.				cilium assembly (GO:0042384)|embryonic body morphogenesis (GO:0010172)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of planar polarity (GO:0001736)|hair follicle development (GO:0001942)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)|negative regulation of neural crest formation (GO:0090301)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|positive regulation of cilium assembly (GO:0045724)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(3)	4		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)		TCTGGGGAGACAGCAGCAGCAGC	0.635																																						ENST00000313777.4																			0				endometrium(1)|lung(3)	4						c.(1180-1182)del		fuzzy planar cell polarity protein																																				SO:0001651	inframe_deletion	80199				cilium assembly|embryonic body morphogenesis|embryonic skeletal system morphogenesis|establishment of planar polarity|hair follicle development|neural tube closure|protein transport|regulation of smoothened signaling pathway	cytoplasm|cytoskeleton		g.chr19:50310483_50310485delCAG	BC016793	CCDS12781.1, CCDS54293.1	19q13.33	2013-03-05	2013-03-05			ENSG00000010361			26219	protein-coding gene	gene with protein product		610622	"""fuzzy homolog (Drosophila)"""			21761479	Standard	NM_001171937		Approved	FLJ22688, Fy	uc002ppq.2	Q9BT04		ENST00000313777.4:c.1180_1182delCTG	19.37:g.50310492_50310494delCAG	ENSP00000313309:p.Leu394del					FUZ_ENST00000528094.1_In_Frame_Del_p.L358del|FUZ_ENST00000533418.1_In_Frame_Del_p.L344del|FUZ_ENST00000445575.2_Intron	p.L394del	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)	11	1343_1345	-		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)	394			Leu-rich.		B2RD86|B5MDH0|Q6PJY0|Q9H613	In_Frame_Del	DEL	ENST00000313777.4	37	c.1180_1182delCTG	CCDS12781.1																																																																																				0.635	FUZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393986.1	NM_025129		14	325						14	325	---	---	---	---
NIFKP6	100132796	broad.mit.edu	37	19	51906669	51906670	+	lincRNA	INS	-	-	T	rs202017245		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr19:51906669_51906670insT	ENST00000600765.1	+	0	324_325																											GGTTGTTCTTGTTTTTTTTGCT	0.446																																						ENST00000600765.1																			0																																																			0							g.chr19:51906669_51906670insT																													19.37:g.51906677_51906677dupT														0	324_325	+									RNA	INS	ENST00000600765.1	37																																																																																						0.446	CTD-2616J11.14-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000465204.1			9	390						9	390	---	---	---	---
GZF1	64412	broad.mit.edu	37	20	23345921	23345923	+	In_Frame_Del	DEL	GAG	GAG	-	rs547594353	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr20:23345921_23345923delGAG	ENST00000338121.5	+	2	978_980	c.901_903delGAG	c.(901-903)gagdel	p.E306del	GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000377051.2_In_Frame_Del_p.E306del			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	306					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					ggaggaggaagaggaggaggagg	0.532																																						ENST00000338121.5																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24						c.(901-903)del		GDNF-inducible zinc finger protein 1				7,68,4189		0,0,7,1,66,2058						-8.0	0.0			52	1,62,8191		0,0,1,3,56,4067	no	codingComplex	GZF1	NM_022482.3		0,0,8,4,122,6125	A1A1,A1A2,A1R,A2A2,A2R,RR		0.7633,1.7589,1.1024				8,130,12380				SO:0001651	inframe_deletion	64412				transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding	g.chr20:23345921_23345923delGAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.901_903delGAG	20.37:g.23345930_23345932delGAG	ENSP00000338290:p.Glu306del					GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000377051.2_In_Frame_Del_p.E306del	p.E306del			Q9H116	GZF1_HUMAN			2	978_980	+	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)		306					A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	In_Frame_Del	DEL	ENST00000338121.5	37	c.901_903delGAG	CCDS13151.1																																																																																				0.532	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		7	414						7	414	---	---	---	---
GINS1	9837	broad.mit.edu	37	20	25422397	25422397	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr20:25422397delA	ENST00000262460.4	+	6	601	c.507delA	c.(505-507)ttafs	p.L169fs	GINS1_ENST00000429262.2_3'UTR	NM_021067.3	NP_066545.3	Q14691	PSF1_HUMAN	GINS complex subunit 1 (Psf1 homolog)	169					DNA strand elongation involved in DNA replication (GO:0006271)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.N172fs*14(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						CAGTCCTATTAAAAAAAAATA	0.299																																						ENST00000262460.4																			1	Deletion - Frameshift(1)	p.N172fs*14(1)	lung(1)	central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						c.(505-507)ttfs		GINS complex subunit 1 (Psf1 homolog)							53.0	59.0	57.0					20																	25422397		2199	4294	6493	SO:0001589	frameshift_variant	9837				DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm		g.chr20:25422397delA	BC012542	CCDS33451.1	20p11.21	2006-05-04			ENSG00000101003	ENSG00000101003			28980	protein-coding gene	gene with protein product		610608				8724849, 8786132	Standard	NM_021067		Approved	KIAA0186, PSF1	uc002wuv.1	Q14691	OTTHUMG00000032124	ENST00000262460.4:c.507delA	20.37:g.25422397delA	ENSP00000262460:p.Leu169fs					GINS1_ENST00000429262.2_3'UTR	p.L169fs	NM_021067.3	NP_066545.3	Q14691	PSF1_HUMAN			6	601	+			169					Q9NQE2|Q9NQI7	Frame_Shift_Del	DEL	ENST00000262460.4	37	c.507delA	CCDS33451.1																																																																																				0.299	GINS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078433.1	NM_021067		11	577						11	577	---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29624034	29624035	+	Intron	INS	-	-	G	rs201117819		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr20:29624034_29624035insG	ENST00000278882.3	+	4	446				FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Frame_Shift_Ins_p.I25fs			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B											endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTTCTCCAATATTGATGAGGGC	0.287																																						ENST00000439954.2																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(73-75)tgafs																																						SO:0001627	intron_variant	0							g.chr20:29624034_29624035insG			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.67-8->G	20.37:g.29624034_29624035insG						FRG1B_ENST00000278882.3_Intron|FRG1B_ENST00000358464.4_Intron	p.*25fs							4	419_420	+								C4AME5	Frame_Shift_Ins	INS	ENST00000278882.3	37	c.73_74insG																																																																																					0.287	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		8	97						8	97	---	---	---	---
CBR3	874	broad.mit.edu	37	21	37510175	37510175	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr21:37510175delT	ENST00000290354.5	+	2	623	c.342delT	c.(340-342)aatfs	p.N114fs	CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000413862.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000608622.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	114					cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	TGAAGACAAATTTTTTTGCCA	0.408																																						ENST00000290354.5																			0				kidney(1)|large_intestine(1)|lung(1)	3						c.(340-342)aafs		carbonyl reductase 3							158.0	149.0	152.0					21																	37510175		2203	4300	6503	SO:0001589	frameshift_variant	874					cytosol|nucleus	carbonyl reductase (NADPH) activity|NADPH binding	g.chr21:37510175delT	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.342delT	21.37:g.37510175delT	ENSP00000290354:p.Asn114fs					CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	p.N114fs	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN			2	623	+			114					Q6FHP2	Frame_Shift_Del	DEL	ENST00000290354.5	37	c.342delT	CCDS13642.1																																																																																				0.408	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1			10	645						10	645	---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45472274	45472275	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr21:45472274_45472275insA	ENST00000291574.4	+	4	574_575	c.399_400insA	c.(400-402)aaafs	p.K134fs	TRAPPC10_ENST00000380221.3_Frame_Shift_Ins_p.K134fs	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	134					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.K133N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ATGATGCCAAGAAAAAAAACAA	0.356																																						ENST00000291574.4																			1	Substitution - Missense(1)	p.K133N(1)	lung(1)	NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						c.(397-402)aaaaaafs		trafficking protein particle complex 10																																				SO:0001589	frameshift_variant	7109				vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity	g.chr21:45472274_45472275insA	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.407dupA	21.37:g.45472282_45472282dupA	ENSP00000291574:p.Lys134fs					TRAPPC10_ENST00000380221.3_Frame_Shift_Ins_p.KK133fs	p.KK133fs	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN			4	574_575	+			133					Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Frame_Shift_Ins	INS	ENST00000291574.4	37	c.399_400insA	CCDS13704.1																																																																																				0.356	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		8	565						8	565	---	---	---	---
SF3A1	10291	broad.mit.edu	37	22	30742328	30742330	+	In_Frame_Del	DEL	CTG	CTG	-	rs141985009	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:30742328_30742330delCTG	ENST00000215793.8	-	3	518_520	c.364_366delCAG	c.(364-366)cagdel	p.Q122del	SF3A1_ENST00000439242.1_Intron	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	122	Poly-Gln.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						GCTGGGTGGTCTGCTGCTGCTGC	0.606																																						ENST00000215793.7																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						c.(364-366)del		splicing factor 3a, subunit 1, 120kDa																																				SO:0001651	inframe_deletion	10291				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding	g.chr22:30742328_30742330delCTG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.364_366delCAG	22.37:g.30742337_30742339delCTG	ENSP00000215793:p.Gln122del					SF3A1_ENST00000439242.1_Intron	p.Q122del	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN			3	518_520	-			122			Poly-Gln.		E9PAW1	In_Frame_Del	DEL	ENST00000215793.8	37	c.364_366delCAG	CCDS13875.1																																																																																				0.606	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		11	626						11	626	---	---	---	---
DNAJB7	150353	broad.mit.edu	37	22	41257115	41257115	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:41257115delT	ENST00000307221.4	-	1	1015	c.884delA	c.(883-885)aagfs	p.K296fs	XPNPEP3_ENST00000482652.1_Intron|XPNPEP3_ENST00000541156.1_Intron|XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000544094.1_5'Flank|XPNPEP3_ENST00000357137.4_Intron	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 7	296	Poly-Lys.						chaperone binding (GO:0051087)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						TTTACGCTTCTTTTTTTTCCT	0.378																																						ENST00000307221.4																			0				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						c.(883-885)agfs		DnaJ (Hsp40) homolog, subfamily B, member 7							105.0	100.0	102.0					22																	41257115		2203	4300	6503	SO:0001589	frameshift_variant	150353				protein folding		heat shock protein binding|unfolded protein binding	g.chr22:41257115delT	AF085232	CCDS14008.1	22q13.2	2011-09-02			ENSG00000172404	ENSG00000172404		"""Heat shock proteins / DNAJ (HSP40)"""	24986	protein-coding gene	gene with protein product		611336				12477932	Standard	NM_145174		Approved	HSC3	uc003azj.3	Q7Z6W7	OTTHUMG00000151202	ENST00000307221.4:c.884delA	22.37:g.41257115delT	ENSP00000307197:p.Lys296fs					XPNPEP3_ENST00000541156.1_Intron|XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000482652.1_Intron|XPNPEP3_ENST00000357137.4_Intron	p.K296fs	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN			1	1015	-			296			Poly-Lys.		Q2M220|Q5H904|Q8WYJ7	Frame_Shift_Del	DEL	ENST00000307221.4	37	c.884delA	CCDS14008.1																																																																																				0.378	DNAJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321765.1	NM_145174		7	490						7	490	---	---	---	---
DNAJB7	150353	broad.mit.edu	37	22	41257834	41257835	+	Frame_Shift_Ins	INS	-	-	A	rs200971397	byFrequency	TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:41257834_41257835insA	ENST00000307221.4	-	1	295_296	c.164_165insT	c.(163-165)gtafs	p.V55fs	XPNPEP3_ENST00000482652.1_3'UTR|XPNPEP3_ENST00000541156.1_Intron|XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000544094.1_5'Flank|XPNPEP3_ENST00000357137.4_Intron	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 7	55	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.						chaperone binding (GO:0051087)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						CATTTGATAATACCTCGTATGC	0.371													A|A|AA|insertion	254	0.0507188	0.003	0.3487	5008	,	,		18040	0.003		0.005	False		,,,				2504	0.0					ENST00000307221.4																			0				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						c.(163-165)gttfs		DnaJ (Hsp40) homolog, subfamily B, member 7			,,	35,4229		1,33,2098					,,	1.4	1.0			221	49,8205		0,49,4078	no	frameshift,intron,utr-3	XPNPEP3,DNAJB7	NM_145174.1,NM_022098.3,NM_001204827.1	,,	1,82,6176	A1A1,A1R,RR		0.5937,0.8208,0.671	,,	,,		84,12434				SO:0001589	frameshift_variant	150353				protein folding		heat shock protein binding|unfolded protein binding	g.chr22:41257834_41257835insA	AF085232	CCDS14008.1	22q13.2	2011-09-02			ENSG00000172404	ENSG00000172404		"""Heat shock proteins / DNAJ (HSP40)"""	24986	protein-coding gene	gene with protein product		611336				12477932	Standard	NM_145174		Approved	HSC3	uc003azj.3	Q7Z6W7	OTTHUMG00000151202	ENST00000307221.4:c.165dupT	22.37:g.41257835_41257835dupA	ENSP00000307197:p.Val55fs					XPNPEP3_ENST00000541156.1_Intron|XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000482652.1_3'UTR|XPNPEP3_ENST00000357137.4_Intron	p.V55fs	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN			1	295_296	-			55			J.		Q2M220|Q5H904|Q8WYJ7	Frame_Shift_Ins	INS	ENST00000307221.4	37	c.164_165insT	CCDS14008.1																																																																																				0.371	DNAJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321765.1	NM_145174		9	1038						9	1038	---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42610573	42610575	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:42610573_42610575delAGG	ENST00000359486.3	-	1	873_875	c.737_739delCCT	c.(736-741)tccttc>ttc	p.S246del	TCF20_ENST00000335626.4_In_Frame_Del_p.S246del	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	246	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GGTGAAGGGAaggaggaggagga	0.507																																						ENST00000359486.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						c.(736-741)ttc>t		transcription factor 20 (AR1)																																				SO:0001651	inframe_deletion	6942				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding	g.chr22:42610573_42610575delAGG	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.737_739delCCT	22.37:g.42610582_42610584delAGG	ENSP00000352463:p.Ser246del					TCF20_ENST00000335626.4_In_Frame_Del_p.SF246del	p.SF246del	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN			1	873_875	-			246			Ser-rich.		A9JX12|O14528|Q13078|Q4V353|Q9H4M0	In_Frame_Del	DEL	ENST00000359486.3	37	c.737_739delCCT	CCDS14033.1																																																																																				0.507	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492		7	455						7	455	---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43213780	43213780	+	Frame_Shift_Del	DEL	T	T	-	rs552164906		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chr22:43213780delT	ENST00000263245.5	-	10	1115	c.896delA	c.(895-897)aatfs	p.N299fs	ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs|ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	299					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGAGTCAACATTTTTTTTGCC	0.363																																					GBM(58;544 1030 21460 27159 48838)	ENST00000263245.5																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						c.(895-897)atfs		ADP-ribosylation factor GTPase activating protein 3							317.0	285.0	296.0					22																	43213780		2203	4300	6503	SO:0001589	frameshift_variant	26286				intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding	g.chr22:43213780delT	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.896delA	22.37:g.43213780delT	ENSP00000263245:p.Asn299fs					ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs|ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs	p.N299fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN			10	1115	-			299					E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Frame_Shift_Del	DEL	ENST00000263245.5	37	c.896delA	CCDS14042.1																																																																																				0.363	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		10	891						10	891	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73047124	73047125	+	lincRNA	DEL	AC	AC	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:73047124_73047125delAC	ENST00000604411.1	+	0	35085_35086				XIST_ENST00000429829.1_lincRNA	NR_003255.2				TSIX transcript, XIST antisense RNA																		GCCACACATGACACACACACAC	0.47																																						ENST00000604411.1																			0																	21,2160		6,4,5,902,352						-3.8	0.0			146	63,3745		10,20,23,1404,917	no	intergenic				16,24,28,2306,1269	A1A1,A1R,A1,RR,R		1.6544,0.9629,1.4026				84,5905						0							g.chrX:73047124_73047125delAC			Xq13.2	2012-10-19	2012-08-15			ENSG00000270641		"""Long non-coding RNAs"", ""-"""	12377	non-coding RNA	RNA, long non-coding	"""XIST antisense RNA (non-protein coding)"", ""long intergenic non-protein coding RNA 13"""	300181	"""X (inactive)-specific transcript, antisense"", ""TSIX transcript, XIST antisense RNA (non-protein coding)"""			10192391	Standard	NR_003255		Approved	NCRNA00013, XIST-AS1, LINC00013	uc004ebn.2				X.37:g.73047134_73047135delAC						XIST_ENST00000429829.1_lincRNA		NR_003255.2						0	35085_35086	+									RNA	DEL	ENST00000604411.1	37																																																																																						0.470	TSIX-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000469120.1	NR_003255		11	496						11	496	---	---	---	---
XIST	7503	broad.mit.edu	37	X	73071723	73071723	+	lincRNA	DEL	G	G	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:73071723delG	ENST00000429829.1	-	0	865					NR_001564.2				X inactive specific transcript (non-protein coding)																		CTCTGCCAAAGCGGTAGGTAC	0.458													G|G|-|deletion	1	0.000264901	0.0008	0.0	3775	,	,		13826	0.0		0.0	False		,,,				2504	0.0					ENST00000429829.1																			0																				150.0	139.0	142.0					X																	73071723		876	1991	2867			0							g.chrX:73071723delG	M97168		Xq13.2	2013-12-18	2013-02-07		ENSG00000229807	ENSG00000229807		"""Long non-coding RNAs"", ""-"""	12810	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 1"""	314670	"""X (inactive)-specific transcript"", ""X (inactive)-specific transcript (non-protein coding)"""	DXS399E		1985261, 2034279	Standard	NR_001564		Approved	NCRNA00001, DXS1089, swd66, LINC00001	uc004ebm.2		OTTHUMG00000021839		X.37:g.73071723delG								NR_001564.2						0	865	-									RNA	DEL	ENST00000429829.1	37																																																																																						0.458	XIST-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000057239.1	NR_001564		11	502						11	502	---	---	---	---
BHLHB9	80823	broad.mit.edu	37	X	102004419	102004421	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:102004419_102004421delGAG	ENST00000372735.1	+	4	1081_1083	c.496_498delGAG	c.(496-498)gagdel	p.E171del	BHLHB9_ENST00000361229.4_In_Frame_Del_p.E171del|BHLHB9_ENST00000457056.1_In_Frame_Del_p.E171del|BHLHB9_ENST00000447531.1_In_Frame_Del_p.E171del|BHLHB9_ENST00000448867.1_In_Frame_Del_p.E171del			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	171	Poly-Glu.				learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GTCAGGGGCTGAGGAGGAGGAGG	0.488																																						ENST00000372735.1																			0				cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(496-498)del		basic helix-loop-helix domain containing, class B, 9																																				SO:0001651	inframe_deletion	80823					cytoplasm|nucleus	binding	g.chrX:102004419_102004421delGAG	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.496_498delGAG	X.37:g.102004428_102004430delGAG	ENSP00000361820:p.Glu171del					BHLHB9_ENST00000457056.1_In_Frame_Del_p.E171del|BHLHB9_ENST00000447531.1_In_Frame_Del_p.E171del|BHLHB9_ENST00000361229.4_In_Frame_Del_p.E171del|BHLHB9_ENST00000448867.1_In_Frame_Del_p.E171del	p.E171del			Q6PI77	BHLH9_HUMAN			4	1081_1083	+			171			Poly-Glu.		Q9C0G2	In_Frame_Del	DEL	ENST00000372735.1	37	c.496_498delGAG	CCDS14502.1																																																																																				0.488	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		15	785						15	785	---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110406206	110406208	+	In_Frame_Del	DEL	GAA	GAA	-	rs374572591		TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:110406206_110406208delGAA	ENST00000372010.1	+	10	1019_1021	c.577_579delGAA	c.(577-579)gaadel	p.E197del	PAK3_ENST00000446737.1_In_Frame_Del_p.E182del|PAK3_ENST00000360648.4_In_Frame_Del_p.E218del|PAK3_ENST00000417227.1_In_Frame_Del_p.E203del|PAK3_ENST00000425146.1_In_Frame_Del_p.E182del|PAK3_ENST00000519681.1_In_Frame_Del_p.E203del|PAK3_ENST00000372007.5_In_Frame_Del_p.E182del|PAK3_ENST00000262836.4_In_Frame_Del_p.E197del|PAK3_ENST00000518291.1_In_Frame_Del_p.E218del			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	197	Linker.|Poly-Glu.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						agatgaagaggaagaagaagaag	0.394										TSP Lung(19;0.15)																												ENST00000519681.1																			0				breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						c.(595-597)del		p21 protein (Cdc42/Rac)-activated kinase 3																																				SO:0001651	inframe_deletion	5063				multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding	g.chrX:110406206_110406208delGAA	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"""mental retardation, X-linked 47"", ""p21 (CDKN1A)-activated kinase 3"""	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.577_579delGAA	X.37:g.110406215_110406217delGAA	ENSP00000361080:p.Glu197del	TSP Lung(19;0.15)				PAK3_ENST00000518291.1_In_Frame_Del_p.E218del|PAK3_ENST00000446737.1_In_Frame_Del_p.E182del|PAK3_ENST00000372010.1_In_Frame_Del_p.E197del|PAK3_ENST00000360648.4_In_Frame_Del_p.E218del|PAK3_ENST00000262836.4_In_Frame_Del_p.E197del|PAK3_ENST00000372007.4_In_Frame_Del_p.E182del|PAK3_ENST00000425146.1_In_Frame_Del_p.E182del|PAK3_ENST00000417227.1_In_Frame_Del_p.E203del	p.E203del			O75914	PAK3_HUMAN			10	1037_1039	+			197			Linker.		A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	In_Frame_Del	DEL	ENST00000372010.1	37	c.595_597delGAA	CCDS48153.1																																																																																				0.394	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		7	528						7	528	---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119694117	119694119	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:119694117_119694119delGAG	ENST00000404115.3	-	3	830_832	c.429_431delCTC	c.(427-432)tcctca>tca	p.143_144SS>S	CUL4B_ENST00000371322.5_In_Frame_Del_p.125_126SS>S|CUL4B_ENST00000336592.6_In_Frame_Del_p.130_131SS>S	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	143	Ser-rich.				cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGGTGAAGATgaggaggaggagg	0.488																																						ENST00000371322.5																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						c.(373-378)tca>tc		cullin 4B			,	18,3703		0,6,12,1586,525					,	-9.6	0.5			58	72,6412		1,19,51,2337,1719	no	coding,coding	CUL4B	NM_003588.3,NM_001079872.1	,	1,25,63,3923,2244	A1A1,A1R,A1,RR,R		1.1104,0.4837,0.8819	,	,		90,10115				SO:0001651	inframe_deletion	8450				cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding	g.chrX:119694117_119694119delGAG	U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.429_431delCTC	X.37:g.119694126_119694128delGAG	ENSP00000384109:p.Ser146del					CUL4B_ENST00000404115.3_In_Frame_Del_p.SS145del|CUL4B_ENST00000336592.6_In_Frame_Del_p.SS132del	p.SS127del	NM_001079872.1	NP_001073341.1	Q13620	CUL4B_HUMAN			1	436_438	-			145			Ser-rich.		B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	In_Frame_Del	DEL	ENST00000404115.3	37	c.375_377delCTC	CCDS35379.1																																																																																				0.488	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058103.1	NM_003588		14	296						14	296	---	---	---	---
SPANXN3	139067	broad.mit.edu	37	X	142605149	142605149	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:142605149delT	ENST00000370503.2	-	1	154	c.71delA	c.(70-72)aatfs	p.N24fs	GS1-256O22.5_ENST00000431432.1_RNA	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN	SPANX family, member N3	24										endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					TACCTCATCATTTTTTTTGTT	0.453																																						ENST00000370503.2																			0				endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|urinary_tract(1)	14						c.(70-72)atfs		SPANX family, member N3							221.0	189.0	200.0					X																	142605149		2203	4300	6503	SO:0001589	frameshift_variant	139067							g.chrX:142605149delT		CCDS35418.1	Xq27.3	2012-06-12			ENSG00000189252	ENSG00000189252			33176	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 8"""	300666				14973187, 17012309	Standard	NM_001009609		Approved	SPANX-N3, CT11.8	uc004fbw.3	Q5MJ09	OTTHUMG00000022582	ENST00000370503.2:c.71delA	X.37:g.142605149delT	ENSP00000359534:p.Asn24fs						p.N24fs	NM_001009609.2	NP_001009609.1	Q5MJ09	SPXN3_HUMAN			1	154	-	Acute lymphoblastic leukemia(192;6.56e-05)		24					Q0ZNK4	Frame_Shift_Del	DEL	ENST00000370503.2	37	c.71delA	CCDS35418.1																																																																																				0.453	SPANXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058620.2	NM_001009609		7	659						7	659	---	---	---	---
SPANXN2	494119	broad.mit.edu	37	X	142803692	142803692	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:142803692delT	ENST00000370498.1	-	1	824	c.71delA	c.(70-72)aatfs	p.N24fs		NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN	SPANX family, member N2	24										NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TACCTCATCATTTTTTTTGTT	0.443																																						ENST00000370498.1																			0				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27						c.(70-72)atfs		SPANX family, member N2				0,17,3704		0,0,0,1,12,3,1579,534	214.0	197.0	202.0			-0.2	0.0	X		204	1,105,6378		0,0,1,7,61,30,2288,1740	no	codingComplex	SPANXN2	NM_001009615.1		0,0,1,8,73,33,3867,2274	A1A1,A1A2,A1R,A2A2,A2R,A2,RR,R		1.6348,0.4569,1.2053			142803692	1,122,10082	2203	4300	6503	SO:0001589	frameshift_variant	494119							g.chrX:142803692delT		CCDS35419.1	Xq27.3	2012-06-12			ENSG00000203924	ENSG00000268988			33175	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 7"""	300665				14973187, 17012309	Standard	NM_001009615		Approved	SPANX-N2, CT11.7	uc004fbz.3	Q5MJ10	OTTHUMG00000022583	ENST00000370498.1:c.71delA	X.37:g.142803692delT	ENSP00000359529:p.Asn24fs						p.N24fs	NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN			1	824	-	Acute lymphoblastic leukemia(192;6.56e-05)		24					Q0ZNM2	Frame_Shift_Del	DEL	ENST00000370498.1	37	c.71delA	CCDS35419.1																																																																																				0.443	SPANXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058621.2	NM_001009615		8	746						8	746	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150817142	150817144	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-IB-7886-01A-11D-2154-08	TCGA-IB-7886-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0ae0d66a-f390-4cd4-aa84-f35e8980a52d	f101fa1b-c3a8-40a0-b4ea-812861d7e7c9	g.chrX:150817142_150817144delGCT	ENST00000370357.4	+	9	930_932	c.685_687delGCT	c.(685-687)gctdel	p.A236del		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	236	Poly-Ala.					nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A229A(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					CGTTGAACCCgctgctgctgctg	0.433																																						ENST00000370357.4																			2	Substitution - coding silent(2)	p.A229A(2)	lung(2)	breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(685-687)del		PAS domain containing 1																																				SO:0001651	inframe_deletion	139135					nucleus	signal transducer activity	g.chrX:150817142_150817144delGCT	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.685_687delGCT	X.37:g.150817151_150817153delGCT	ENSP00000359382:p.Ala236del						p.A236del	NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN			9	930_932	+	Acute lymphoblastic leukemia(192;6.56e-05)		236			Poly-Ala.		Q3MNE0|Q69HD7|Q8N7X9	In_Frame_Del	DEL	ENST00000370357.4	37	c.685_687delGCT	CCDS35431.1																																																																																				0.433	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		12	506						12	506	---	---	---	---
