#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
KAT6A	7994	broad.mit.edu	37	8	41790659	41790659	+	Silent	SNP	T	T	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:41790659T>G	ENST00000396930.3	-	18	5622	c.5079A>C	c.(5077-5079)ccA>ccC	p.P1693P	KAT6A_ENST00000406337.1_Silent_p.P1693P|KAT6A_ENST00000265713.2_Silent_p.P1693P	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1693	Gln/Pro-rich.|Interaction with PML.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ggggagggggtgggggtggag	0.627																																						ENST00000396930.3																			0											c.(5077-5079)ccA>ccC		K(lysine) acetyltransferase 6A							16.0	18.0	18.0					8																	41790659		2196	4293	6489	SO:0001819	synonymous_variant	7994				histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding	g.chr8:41790659T>G	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.5079A>C	8.37:g.41790659T>G						KAT6A_ENST00000406337.1_Silent_p.P1693P|KAT6A_ENST00000265713.2_Silent_p.P1693P	p.P1693P	NM_001099412.1	NP_001092882.1	Q92794	MYST3_HUMAN			18	5622	-			1693			Gln/Pro-rich.		Q76L81	Silent	SNP	ENST00000396930.3	37	c.5079A>C	CCDS6124.1																																																																																				0.627	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		15	118	0	0	0	1	0	15	118				
TBC1D4	9882	broad.mit.edu	37	13	75884223	75884223	+	Silent	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:75884223C>T	ENST00000377636.3	-	14	2794	c.2448G>A	c.(2446-2448)ccG>ccA	p.P816P	TBC1D4_ENST00000425511.1_Silent_p.P33P|TBC1D4_ENST00000377625.2_Silent_p.P753P|TBC1D4_ENST00000431480.2_Silent_p.P808P	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	816					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		ATACAACCAGCGGTTCCTCCT	0.493																																						ENST00000377636.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						c.(2446-2448)ccG>ccA		TBC1 domain family, member 4							77.0	70.0	72.0					13																	75884223		1869	4097	5966	SO:0001819	synonymous_variant	9882					cytoplasm	Rab GTPase activator activity	g.chr13:75884223C>T	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2448G>A	13.37:g.75884223C>T						TBC1D4_ENST00000431480.2_Silent_p.P808P|TBC1D4_ENST00000377625.2_Silent_p.P753P|TBC1D4_ENST00000425511.1_Silent_p.P33P	p.P816P	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN		GBM - Glioblastoma multiforme(99;0.0116)	14	2794	-		Prostate(6;0.014)|Breast(118;0.0982)	816					A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	c.2448G>A	CCDS41901.1																																																																																				0.493	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		20	232	0	0	0	1	0	20	232				
MALAT1	378938	broad.mit.edu	37	11	65268712	65268712	+	lincRNA	SNP	T	T	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:65268712T>G	ENST00000534336.1	+	0	3480				AP000769.7_ENST00000602344.1_lincRNA	NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		TTTGTGGGGGTGGGGGCAAAA	0.393																																						ENST00000534336.1																			0																																																			0							g.chr11:65268712T>G	AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65268712T>G								NR_002819.2						0	3480	+									RNA	SNP	ENST00000534336.1	37																																																																																						0.393	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1	NR_002819		44	173	0	0	0	1	0	44	173				
ARHGEF10L	55160	broad.mit.edu	37	1	18023723	18023723	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:18023723G>A	ENST00000361221.3	+	29	3847	c.3688G>A	c.(3688-3690)Gcc>Acc	p.A1230T	ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A933T|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A1003T|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1191T	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	1230						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CGCCCGCGACGCCCACCGCAA	0.677																																						ENST00000361221.3																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43						c.(3688-3690)Gcc>Acc		Rho guanine nucleotide exchange factor (GEF) 10-like							24.0	25.0	25.0					1																	18023723		2189	4258	6447	SO:0001583	missense	55160				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity	g.chr1:18023723G>A	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.3688G>A	1.37:g.18023723G>A	ENSP00000355060:p.Ala1230Thr					ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A933T|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A1003T	p.A1230T	NM_018125.3	NP_060595.3	Q9HCE6	ARGAL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)	29	3847	+		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)	1230					B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	c.3688G>A	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293646	0.80914	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000375415;ENST00000375408;ENST00000167825	T;T;T;T;T	0.61510	0.35;0.39;0.39;0.1;2.37	5.0	3.13	0.36017	.	0.166885	0.39544	N	0.001340	T	0.64929	0.2643	L	0.52364	1.645	0.39278	D	0.964508	P;D;P;D;D;D	0.89917	0.669;0.979;0.669;0.999;1.0;1.0	B;B;B;P;D;D	0.71870	0.115;0.389;0.115;0.847;0.975;0.961	T	0.61898	-0.6968	10	0.33141	T	0.24	-14.259	8.6006	0.33742	0.1809:0.0:0.8191:0.0	.	1003;933;991;1186;1191;1230	Q5VXI4;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;ARGAL_HUMAN	T	1230;1191;1191;1003;933	ENSP00000355060:A1230T;ENSP00000399401:A1191T;ENSP00000364564:A1191T;ENSP00000364557:A1003T;ENSP00000167825:A933T	ENSP00000167825:A933T	A	+	1	0	ARHGEF10L	17896310	0.538000	0.26394	0.984000	0.44739	0.967000	0.64934	1.279000	0.33191	0.507000	0.28148	-0.136000	0.14681	GCC		0.677	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		16	243	0	0	0	1	0	16	243				
SGMS1-AS1	104355295	broad.mit.edu	37	10	52390836	52390836	+	RNA	SNP	A	A	G	rs7904101	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:52390836A>G	ENST00000443374.2	+	0	2025				RP11-50E11.3_ENST00000609579.1_RNA																							TTCCGTATCCATATTCTACAA	0.512													A|||	3854	0.769569	0.9047	0.6542	5008	,	,		16952	0.6885		0.6998	False		,,,				2504	0.8241					ENST00000443374.1																			0																																																			0							g.chr10:52390836A>G																													10.37:g.52390836A>G														0	1529	+									RNA	SNP	ENST00000443374.2	37																																																																																						0.512	RP11-50E11.3-001	KNOWN	basic	antisense	antisense	OTTHUMT00000048071.2			8	88	0	0	0	1	0	8	88				
CSHL1	1444	broad.mit.edu	37	17	61987405	61987405	+	Intron	SNP	A	A	T	rs2006122	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:61987405A>T	ENST00000309894.5	-	4	471				CSHL1_ENST00000346606.6_Intron|CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000259003.10_Intron|CSHL1_ENST00000438387.2_Intron|CSHL1_ENST00000561003.1_Silent_p.P113P|CSHL1_ENST00000450719.3_Silent_p.P102P|CSHL1_ENST00000558099.1_5'UTR	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1							extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						ATGAAGAATAAGGTGAGTTCT	0.547													A|||	987	0.197085	0.2731	0.196	5008	,	,		19953	0.0794		0.2624	False		,,,				2504	0.1493					ENST00000450719.3																			0				endometrium(3)|lung(6)	9						c.(304-306)ccT>ccA		chorionic somatomammotropin hormone-like 1																																				SO:0001627	intron_variant	1444					extracellular region	hormone activity|metal ion binding	g.chr17:61987405A>T	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.471+116T>A	17.37:g.61987405A>T						CSHL1_ENST00000309894.5_Intron|CSHL1_ENST00000346606.6_Intron|CSHL1_ENST00000561003.1_Silent_p.P113P|CSHL1_ENST00000438387.2_Intron|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Intron|CSHL1_ENST00000392824.4_3'UTR	p.P102P			Q14406	CSHL_HUMAN			3	543	-			0					D3DU26|D3DU27|Q0VDB2	Silent	SNP	ENST00000309894.5	37	c.306T>A	CCDS11652.1																																																																																				0.547	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579		35	673	0	0	0	1	0	35	673				
PCYT2	5833	broad.mit.edu	37	17	79866486	79866486	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:79866486C>T	ENST00000538936.2	-	4	473	c.365G>A	c.(364-366)gGc>gAc	p.G122D	PCYT2_ENST00000331285.3_Missense_Mutation_p.G44D|PCYT2_ENST00000538721.2_Missense_Mutation_p.G122D|PCYT2_ENST00000570388.1_Missense_Mutation_p.G44D|PCYT2_ENST00000570391.1_Missense_Mutation_p.G90D|PCYT2_ENST00000571105.1_Missense_Mutation_p.G122D	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	122					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	GGTGTCCCGGCCATCTACAGT	0.597																																						ENST00000538936.2																			0				breast(2)|endometrium(1)|lung(4)|ovary(1)	8						c.(364-366)gGc>gAc		phosphate cytidylyltransferase 2, ethanolamine							117.0	98.0	105.0					17																	79866486		2202	4300	6502	SO:0001583	missense	5833				phospholipid biosynthetic process		ethanolamine-phosphate cytidylyltransferase activity	g.chr17:79866486C>T	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.365G>A	17.37:g.79866486C>T	ENSP00000439245:p.Gly122Asp					PCYT2_ENST00000331285.3_Missense_Mutation_p.G44D|PCYT2_ENST00000538721.2_Missense_Mutation_p.G122D|PCYT2_ENST00000571105.1_Missense_Mutation_p.G122D|PCYT2_ENST00000570388.1_Missense_Mutation_p.G44D|PCYT2_ENST00000570391.1_Missense_Mutation_p.G90D	p.G122D	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		4	473	-	all_neural(118;0.0878)|Ovarian(332;0.12)		122			Catalytic 1 (Potential).		B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Missense_Mutation	SNP	ENST00000538936.2	37	c.365G>A	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.925191	0.92319	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	D;D	0.96396	-4.0;-4.0	4.61	4.61	0.57282	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	M	0.93594	3.435	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0	D	0.99780	1.1027	10	0.87932	D	0	-34.8642	17.6458	0.88148	0.0:1.0:0.0:0.0	.	90;90;122;44;122	B7Z4W6;B7ZAS0;F5H8B1;B7Z7A5;Q99447	.;.;.;.;PCY2_HUMAN	D	122;122;44	ENSP00000442050:G122D;ENSP00000439245:G122D	ENSP00000331719:G44D	G	-	2	0	PCYT2	77459778	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	5.058000	0.64300	2.380000	0.81148	0.650000	0.86243	GGC		0.597	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861		13	171	0	0	0	1	0	13	171				
HMGN2P46	283651	broad.mit.edu	37	15	45848224	45848224	+	lincRNA	SNP	G	G	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:45848224G>T	ENST00000557965.1	+	0	0				HMGN2P46_ENST00000409454.1_RNA																							TGCAGATTTTGTTTAGCTTTT	0.318																																						ENST00000409454.1																			0																																																			0							g.chr15:45848224G>T																													15.37:g.45848224G>T														0	1219	+									RNA	SNP	ENST00000557965.1	37																																																																																						0.318	RP11-96O20.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000416553.1			20	108	1	0	9.22233e-05	1	9.22233e-05	20	108				
IGLV2-28	28812	broad.mit.edu	37	22	23006961	23006961	+	RNA	SNP	C	C	T	rs200228350	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:23006961C>T	ENST00000385099.1	+	0	64																											GGCTCTGCTCCTCCTCACCCT	0.627																																						ENST00000385099.1																			0																																																			0							g.chr22:23006961C>T																													22.37:g.23006961C>T														0	64	+									RNA	SNP	ENST00000385099.1	37																																																																																						0.627	D86994.2-201	NOVEL	basic	miRNA	miRNA				7	55	0	0	0	1	0	7	55				
SPAG4	6676	broad.mit.edu	37	20	34204182	34204182	+	Missense_Mutation	SNP	A	A	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:34204182A>G	ENST00000374273.3	+	1	369	c.257A>G	c.(256-258)aAc>aGc	p.N86S		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	86					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CGGAGCCACAACTGGCAGACA	0.736																																						ENST00000374273.3																			0				NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21						c.(256-258)aAc>aGc		sperm associated antigen 4							4.0	7.0	6.0					20																	34204182		1811	3791	5602	SO:0001583	missense	6676				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity	g.chr20:34204182A>G	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.257A>G	20.37:g.34204182A>G	ENSP00000363391:p.Asn86Ser						p.N86S	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.0127)		1	369	+	Lung NSC(9;0.0053)|all_lung(11;0.00785)		86					O43648	Missense_Mutation	SNP	ENST00000374273.3	37	c.257A>G	CCDS13259.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.867046	0.32977	.	.	ENSG00000061656	ENST00000374273	T	0.13778	2.56	4.62	-0.622	0.11560	.	0.444886	0.20171	N	0.097736	T	0.07548	0.0190	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.23048	-1.0199	10	0.49607	T	0.09	-15.5229	4.3605	0.11199	0.4206:0.3763:0.2031:0.0	.	86	Q9NPE6	SPAG4_HUMAN	S	86	ENSP00000363391:N86S	ENSP00000363391:N86S	N	+	2	0	SPAG4	33667596	0.094000	0.21725	0.452000	0.26994	0.806000	0.45545	0.219000	0.17641	0.001000	0.14605	0.459000	0.35465	AAC		0.736	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		6	52	0	0	0	1	0	6	52				
GRIN2A	2903	broad.mit.edu	37	16	10274206	10274206	+	Silent	SNP	C	C	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:10274206C>T	ENST00000396573.2	-	3	372	c.63G>A	c.(61-63)ccG>ccA	p.P21P	GRIN2A_ENST00000404927.2_Silent_p.P21P|GRIN2A_ENST00000330684.3_Silent_p.P21P|GRIN2A_ENST00000396575.2_Silent_p.P21P|GRIN2A_ENST00000562109.1_Silent_p.P21P	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	21					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGCTCGGCGCCGGACCGCGCC	0.647																																						ENST00000396573.2																			0				NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198						c.(61-63)ccG>ccA		glutamate receptor, ionotropic, N-methyl D-aspartate 2A	Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)						16.0	20.0	19.0					16																	10274206		2189	4283	6472	SO:0001819	synonymous_variant	0				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding	g.chr16:10274206C>T		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.63G>A	16.37:g.10274206C>T						GRIN2A_ENST00000330684.3_Silent_p.P21P|GRIN2A_ENST00000562109.1_Silent_p.P21P|GRIN2A_ENST00000396575.2_Silent_p.P21P|GRIN2A_ENST00000404927.2_Silent_p.P21P	p.P21P	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN			3	372	-			21					O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	c.63G>A	CCDS10539.1																																																																																				0.647	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			16	220	0	0	0	1	0	16	220				
SLC9A7P1	121456	broad.mit.edu	37	12	98849029	98849029	+	RNA	SNP	G	G	T	rs185356002		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:98849029G>T	ENST00000554295.1	-	0	1894					NR_033801.1				solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7 pseudogene 1																		GGGAGCCGCTGTGTCTCCACC	0.592																																						ENST00000554295.1																			0																																																			0							g.chr12:98849029G>T			12q23.1	2013-05-22	2012-03-22		ENSG00000227825	ENSG00000227825		"""Solute carriers"""	32679	pseudogene	pseudogene			"""solute carrier family 9 (sodium/hydrogen exchanger), member 7 pseudogene 1"""				Standard	NR_033801		Approved		uc009ztm.2		OTTHUMG00000170629		12.37:g.98849029G>T								NR_033801.1						0	1894	-									RNA	SNP	ENST00000554295.1	37																																																																																						0.592	SLC9A7P1-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000409869.1			11	47	1	0	7.07596e-05	1	7.30422e-05	11	47				
KRTAP4-9	100132386	broad.mit.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:39261693A>T	ENST00000391415.1	+	1	110	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.D18V(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						TGCGGCCAAGACCTCTGTCAG	0.627																																						ENST00000391415.1																			1	Substitution - Missense(1)	p.D18V(1)	endometrium(1)	central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						c.(52-54)gAc>gTc		keratin associated protein 4-9							18.0	22.0	21.0					17																	39261693		692	1590	2282	SO:0001583	missense	100132386					keratin filament		g.chr17:39261693A>T	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.53A>T	17.37:g.39261693A>T	ENSP00000375234:p.Asp18Val						p.D18V	NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN			1	110	+			18						Missense_Mutation	SNP	ENST00000391415.1	37	c.53A>T	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	6.082	0.383461	0.11524	.	.	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32272	1.46	2.51	0.174	0.15040	.	.	.	.	.	T	0.25865	0.0630	M	0.64404	1.975	0.30580	P	0.762648	B	0.17852	0.024	B	0.14023	0.01	T	0.23154	-1.0196	8	0.45353	T	0.12	.	3.5681	0.07907	0.2702:0.2037:0.5261:0.0	.	18	Q9BYQ8	KRA49_HUMAN	V	18	ENSP00000375234:D18V	ENSP00000334461:D18V	D	+	2	0	KRTAP4-9	36515219	0.000000	0.05858	0.388000	0.26195	0.320000	0.28249	0.098000	0.15189	-0.245000	0.09625	0.155000	0.16302	GAC		0.627	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		28	260	0	0	0	1	0	28	260				
GLB1L3	112937	broad.mit.edu	37	11	134182352	134182352	+	Missense_Mutation	SNP	G	G	A	rs376238782		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:134182352G>A	ENST00000431683.2	+	14	1397	c.1397G>A	c.(1396-1398)cGc>cAc	p.R466H		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	466					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		TCCGGAGGCCGCCTCCGTGCC	0.607																																						ENST00000431683.2																			0				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13						c.(1396-1398)cGc>cAc		galactosidase, beta 1-like 3		G	HIS/ARG	0,4206		0,0,2103	38.0	41.0	40.0		1397	-9.4	0.0	11		40	1,8443		0,1,4221	no	missense	GLB1L3	NM_001080407.2	29	0,1,6324	AA,AG,GG		0.0118,0.0,0.0079	benign	466/654	134182352	1,12649	2103	4222	6325	SO:0001583	missense	112937				carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds	g.chr11:134182352G>A		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1397G>A	11.37:g.134182352G>A	ENSP00000396615:p.Arg466His						p.R466H	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)	14	1397	+	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)	466					A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	c.1397G>A	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	6.749	0.507092	0.12883	0.0	1.18E-4	ENSG00000166105	ENST00000431683	D	0.92752	-3.1	4.69	-9.38	0.00623	.	5.286760	0.00166	N	0.000000	D	0.83760	0.5324	L	0.28400	0.85	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.71444	-0.4591	10	0.44086	T	0.13	.	4.4312	0.11529	0.0864:0.1553:0.3909:0.3674	.	466	Q8NCI6	GLBL3_HUMAN	H	466	ENSP00000396615:R466H	ENSP00000396615:R466H	R	+	2	0	GLB1L3	133687562	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.437000	0.02419	-3.768000	0.00109	-1.608000	0.00805	CGC		0.607	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		18	213	0	0	0	1	0	18	213				
ATXN3L	92552	broad.mit.edu	37	X	13337260	13337260	+	Missense_Mutation	SNP	T	T	C			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:13337260T>C	ENST00000380622.2	-	1	1258	c.794A>G	c.(793-795)gAt>gGt	p.D265G	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	265					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTTTGGAAGATCTTGCGATGT	0.428																																						ENST00000380622.2																			0				endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						c.(793-795)gAt>gGt		ataxin 3-like							345.0	294.0	310.0					X																	13337260		1568	3582	5150	SO:0001583	missense	92552				protein deubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ubiquitin-specific protease activity	g.chrX:13337260T>C		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.794A>G	X.37:g.13337260T>C	ENSP00000369996:p.Asp265Gly					GS1-600G8.3_ENST00000431486.1_RNA	p.D265G	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN			1	1258	-			265					B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	c.794A>G	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	t	7.958	0.746349	0.15710	.	.	ENSG00000123594	ENST00000380622	T	0.70869	-0.52	0.793	0.793	0.18632	.	0.520162	0.22506	N	0.059168	T	0.52484	0.1737	L	0.29908	0.895	0.22017	N	0.99941	P	0.41313	0.745	B	0.38880	0.284	T	0.49390	-0.8945	10	0.72032	D	0.01	.	5.5756	0.17220	0.0:0.0:0.0:1.0	.	265	Q9H3M9	ATX3L_HUMAN	G	265	ENSP00000369996:D265G	ENSP00000369996:D265G	D	-	2	0	ATXN3L	13247181	0.112000	0.22096	0.277000	0.24703	0.064000	0.16182	0.777000	0.26718	0.549000	0.28973	0.341000	0.21757	GAT		0.428	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		69	941	0	0	0	1	0	69	941				
ADAMTS4	9507	broad.mit.edu	37	1	161166457	161166457	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:161166457G>A	ENST00000367996.5	-	2	1275	c.847C>T	c.(847-849)Ccc>Tcc	p.P283S	NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Missense_Mutation_p.P283S	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	283	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GCAGCACTGGGCCCCACTTGG	0.632																																						ENST00000367996.4																			0				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43						c.(847-849)Ccc>Tcc		ADAM metallopeptidase with thrombospondin type 1 motif, 4							65.0	72.0	70.0					1																	161166457		2203	4300	6503	SO:0001583	missense	9507				proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding	g.chr1:161166457G>A	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.847C>T	1.37:g.161166457G>A	ENSP00000356975:p.Pro283Ser					ADAMTS4_ENST00000367995.3_Missense_Mutation_p.P283S	p.P283S	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00275)		2	1275	-	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		283			Peptidase M12B.		Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	c.847C>T	CCDS1223.1	.	.	.	.	.	.	.	.	.	.	G	1.536	-0.543024	0.04053	.	.	ENSG00000158859	ENST00000367996;ENST00000367995	D;D	0.85556	-2.0;-2.0	5.02	4.1	0.47936	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.197780	0.34932	N	0.003569	T	0.53674	0.1811	N	0.11789	0.175	0.39026	D	0.959836	B;B	0.17667	0.014;0.023	B;B	0.16722	0.005;0.016	T	0.50988	-0.8762	10	0.17369	T	0.5	.	9.3761	0.38283	0.1728:0.0:0.8272:0.0	.	283;283	Q5VTW1;O75173	.;ATS4_HUMAN	S	283	ENSP00000356975:P283S;ENSP00000356974:P283S	ENSP00000356974:P283S	P	-	1	0	ADAMTS4	159433081	0.000000	0.05858	0.959000	0.39883	0.998000	0.95712	-0.310000	0.08135	1.350000	0.45770	0.555000	0.69702	CCC		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099		46	515	0	0	0	1	0	46	515				
IGLV2-28	28812	broad.mit.edu	37	22	23006960	23006960	+	RNA	SNP	C	C	A	rs199838243	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:23006960C>A	ENST00000385099.1	+	0	63																											GGGCTCTGCTCCTCCTCACCC	0.627																																						ENST00000385099.1																			0																																																			0							g.chr22:23006960C>A																													22.37:g.23006960C>A														0	63	+									RNA	SNP	ENST00000385099.1	37																																																																																						0.627	D86994.2-201	NOVEL	basic	miRNA	miRNA				7	56	1	0	2.74318e-10	1	2.92606e-10	7	56				
CHD6	84181	broad.mit.edu	37	20	40127944	40127944	+	Silent	SNP	A	A	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:40127944A>G	ENST00000373233.3	-	6	1083	c.906T>C	c.(904-906)acT>acC	p.T302T	CHD6_ENST00000309279.7_Silent_p.T302T|CHD6_ENST00000373222.3_Silent_p.T337T	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	302	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTCCTGGACAGTCTTAGATG	0.398																																						ENST00000373233.3																			0				breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129						c.(904-906)acT>acC		chromodomain helicase DNA binding protein 6							79.0	66.0	71.0					20																	40127944		2203	4300	6503	SO:0001819	synonymous_variant	0				chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding	g.chr20:40127944A>G	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.906T>C	20.37:g.40127944A>G						CHD6_ENST00000373222.3_Silent_p.T337T|CHD6_ENST00000309279.7_Silent_p.T302T	p.T302T	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN			6	1083	-		Myeloproliferative disorder(115;0.00425)	302			Chromo 1.		Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	c.906T>C	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.275613	0.23307	.	.	ENSG00000124177	ENST00000440697	.	.	.	4.44	-6.54	0.01860	.	.	.	.	.	T	0.46386	0.1390	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47711	-0.9096	4	.	.	.	-6.3713	6.0898	0.19989	0.1718:0.214:0.5181:0.0962	.	.	.	.	P	5	.	.	L	-	2	0	CHD6	39561358	0.465000	0.25815	0.861000	0.33841	0.991000	0.79684	-0.339000	0.07832	-1.366000	0.02155	0.459000	0.35465	CTG		0.398	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			7	66	0	0	0	1	0	7	66				
RRN3P2	653390	broad.mit.edu	37	16	29110458	29110458	+	RNA	SNP	T	T	C	rs561841139		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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		20	217	0	0	0	1	0	20	217				
TRIOBP	11078	broad.mit.edu	37	22	38120431	38120431	+	Missense_Mutation	SNP	A	A	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:38120431A>T	ENST00000406386.3	+	7	2123	c.1868A>T	c.(1867-1869)aAc>aTc	p.N623I		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	623					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					ACACGAGATAACCCCAGAACA	0.587																																						ENST00000406386.3																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(1867-1869)aAc>aTc		TRIO and F-actin binding protein							124.0	139.0	134.0					22																	38120431		1943	4152	6095	SO:0001583	missense	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38120431A>T	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1868A>T	22.37:g.38120431A>T	ENSP00000384312:p.Asn623Ile					RP1-37E16.12_ENST00000455236.1_RNA	p.N623I	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN			7	2123	+	Melanoma(58;0.0574)		623					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	c.1868A>T	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	9.134	1.012121	0.19277	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.17	-0.564	0.11774	.	.	.	.	.	T	0.11922	0.0290	L	0.46157	1.445	0.09310	N	1	P	0.38565	0.637	B	0.23574	0.047	T	0.21211	-1.0252	9	0.56958	D	0.05	.	2.4349	0.04480	0.5132:0.2956:0.1911:0.0	.	623	Q9H2D6	TARA_HUMAN	I	623	ENSP00000384312:N623I	ENSP00000384312:N623I	N	+	2	0	TRIOBP	36450377	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	-2.334000	0.01107	0.103000	0.17682	0.254000	0.18369	AAC		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			54	821	0	0	0	1	0	54	821				
LOC644669	644669	broad.mit.edu	37	18	15316755	15316755	+	RNA	SNP	G	G	C	rs200825145		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr18:15316755G>C	ENST00000455308.2	-	0	668					NR_027417.1																						TGTTCCTTCAGATGTTCCTTC	0.433																																						ENST00000455308.2																			0																																																			0							g.chr18:15316755G>C																													18.37:g.15316755G>C								NR_027417.1						0	668	-									RNA	SNP	ENST00000455308.2	37																																																																																						0.433	AP005901.1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373635.1			6	68	0	0	0	1	0	6	68				
VAMP3	9341	broad.mit.edu	37	1	7838212	7838214	+	In_Frame_Del	DEL	TCA	TCA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:7838212_7838214delTCA	ENST00000054666.6	+	4	381_383	c.266_268delTCA	c.(265-270)ttcatc>ttc	p.I94del	VAMP3_ENST00000470357.1_In_Frame_Del_p.I66del|RP3-467L1.6_ENST00000602406.1_RNA	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN	vesicle-associated membrane protein 3	94					calcium ion-dependent exocytosis (GO:0017156)|exocytosis (GO:0006887)|Golgi to plasma membrane protein transport (GO:0043001)|membrane fusion (GO:0061025)|positive regulation of receptor recycling (GO:0001921)|protein complex assembly (GO:0006461)|retrograde transport, endosome to Golgi (GO:0042147)|SNARE complex assembly (GO:0035493)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synapse (GO:0045202)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		CTGGTTATCTTCATCATCATCAT	0.365																																						ENST00000054666.6																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)	6						c.(265-270)ttc>t		vesicle-associated membrane protein 3																																				SO:0001651	inframe_deletion	9341				cellular membrane fusion|positive regulation of receptor recycling|protein complex assembly|protein transport|retrograde transport, endosome to Golgi|substrate adhesion-dependent cell spreading|vesicle docking involved in exocytosis	cell junction|clathrin-coated vesicle|integral to membrane|recycling endosome|synapse|synaptosome	protein binding	g.chr1:7838212_7838214delTCA	BC003570	CCDS88.1	1p36.23	2013-02-13	2012-10-17		ENSG00000049245	ENSG00000049245		"""Vesicle-associated membrane proteins"""	12644	protein-coding gene	gene with protein product	"""cellubrevin"""	603657				9885218	Standard	NM_004781		Approved	CEB	uc001aol.3	Q15836	OTTHUMG00000001225	ENST00000054666.6:c.266_268delTCA	1.37:g.7838221_7838223delTCA	ENSP00000054666:p.Ile94del					VAMP3_ENST00000470357.1_In_Frame_Del_p.FI61del	p.FI89del	NM_004781.3	NP_004772.1	Q15836	VAMP3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)	4	381_383	+	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)	89					Q9BRV4	In_Frame_Del	DEL	ENST00000054666.6	37	c.266_268delTCA	CCDS88.1																																																																																				0.365	VAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003625.1	NM_004781		7	968						7	968	---	---	---	---
KDF1	126695	broad.mit.edu	37	1	27277240	27277241	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:27277240_27277241delTG	ENST00000320567.5	-	3	1134_1135	c.1046_1047delCA	c.(1045-1047)acafs	p.T349fs		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		349					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		AGATCTGCACTGTCAGCTCTAG	0.569																																						ENST00000320567.5																			0				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17						c.(1045-1047)afs		chromosome 1 open reading frame 172																																				SO:0001589	frameshift_variant	126695							g.chr1:27277240_27277241delTG																												ENST00000320567.5:c.1046_1047delCA	1.37:g.27277240_27277241delTG	ENSP00000319179:p.Thr349fs						p.T349fs	NM_152365.2	NP_689578.2	Q8NAX2	CA172_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)	3	1134_1135	-		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)	349					Q5QP32|Q8N0S7	Frame_Shift_Del	DEL	ENST00000320567.5	37	c.1046_1047delCA	CCDS293.1																																																																																				0.569	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1			10	621						10	621	---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35846959	35846960	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:35846959_35846960insA	ENST00000314607.6	+	8	1361_1362	c.1281_1282insA	c.(1282-1284)aaafs	p.K428fs	ZMYM4_ENST00000373297.2_Frame_Shift_Ins_p.K428fs	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	428					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CATATGAACTGAAAAAAAAACC	0.342																																						ENST00000314607.6																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54						c.(1279-1284)ctaaaafs		zinc finger, MYM-type 4																																				SO:0001589	frameshift_variant	9202				multicellular organismal development		DNA binding|zinc ion binding	g.chr1:35846959_35846960insA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1290dupA	1.37:g.35846968_35846968dupA	ENSP00000322915:p.Lys428fs					ZMYM4_ENST00000373297.2_Frame_Shift_Ins_p.LK427fs	p.LK427fs	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN			8	1361_1362	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)	427					A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Frame_Shift_Ins	INS	ENST00000314607.6	37	c.1281_1282insA	CCDS389.1																																																																																				0.342	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		11	406						11	406	---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74575212	74575213	+	Frame_Shift_Ins	INS	-	-	T	rs375424853		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:74575212_74575213insT	ENST00000395089.1	-	4	731_732	c.732_733insA	c.(730-735)aaacagfs	p.Q245fs	LRRIQ3_ENST00000354431.4_Frame_Shift_Ins_p.Q245fs|LRRIQ3_ENST00000370909.2_Frame_Shift_Ins_p.Q137fs|LRRIQ3_ENST00000468759.1_5'UTR			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	245				QQEKII -> TAGKNY (in Ref. 1; BAD18621). {ECO:0000305}.						NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						TTTTCCTGCTGTTTTTTTTTGT	0.327																																						ENST00000354431.4																			0				NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						c.(730-735)aaagcafs		leucine-rich repeats and IQ motif containing 3																																				SO:0001589	frameshift_variant	127255							g.chr1:74575212_74575213insT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.733dupA	1.37:g.74575221_74575221dupT	ENSP00000378524:p.Gln245fs					LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000395089.1_Frame_Shift_Ins_p.A245fs|LRRIQ3_ENST00000370909.2_Frame_Shift_Ins_p.A137fs	p.A245fs	NM_001105659.1	NP_001099129.1	A6PVS8	LRIQ3_HUMAN			5	923_924	-			245	QQEKII -> TAGKNY (in Ref. 1; BAD18621).				A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Frame_Shift_Ins	INS	ENST00000395089.1	37	c.732_733insA	CCDS41350.1																																																																																				0.327	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		20	379						20	379	---	---	---	---
LRRC53	100144878	broad.mit.edu	37	1	74957824	74957826	+	Intron	DEL	CTT	CTT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:74957824_74957826delCTT	ENST00000294635.4	-	2	89				TNNI3K_ENST00000370891.2_In_Frame_Del_p.S847del|FPGT-TNNI3K_ENST00000557284.2_In_Frame_Del_p.S860del|TNNI3K_ENST00000326637.3_In_Frame_Del_p.S746del			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53							integral component of membrane (GO:0016021)				NS(1)|breast(1)|lung(2)	4						TCTCTCTCACCTTCTTCTTCTTC	0.473																																						ENST00000370891.2																			0				cervix(1)|endometrium(3)|kidney(5)|large_intestine(21)|lung(31)|ovary(4)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	76						c.(2527-2532)cct>c		TNNI3 interacting kinase			,	16,4250		8,0,2125					,	5.6	1.0			204	28,8226		13,2,4112	no	coding,coding	TNNI3K,FPGT-TNNI3K	NM_015978.2,NM_001112808.2	,	21,2,6237	A1A1,A1R,RR		0.3392,0.3751,0.3514	,	,		44,12476				SO:0001627	intron_variant	51086							g.chr1:74957824_74957826delCTT			1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621			25255	protein-coding gene	gene with protein product							Standard			Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.26-8765AAG>-	1.37:g.74957833_74957835delCTT						FPGT-TNNI3K_ENST00000557284.1_In_Frame_Del_p.PS843del|TNNI3K_ENST00000326637.3_In_Frame_Del_p.PS742del|LRRC53_ENST00000294635.4_Intron	p.PS843del	NM_001112808.2	NP_001106279.1					25	2544_2546	+									In_Frame_Del	DEL	ENST00000294635.4	37	c.2528_2530delCTT																																																																																					0.473	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000026515.2			9	1149						9	1149	---	---	---	---
BCL10	8915	broad.mit.edu	37	1	85736511	85736511	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:85736511delT	ENST00000370580.1	-	2	873	c.136delA	c.(136-138)atafs	p.I46fs		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	46	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.I46fs*4(1)		haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CTACTGAGTATTTTTTTTGCA	0.343			T	IGH@	MALT																																NSCLC(34;993 1034 12176 32621 50182)	ENST00000370580.1				Dom	yes		1	1p22	8915	T	B-cell CLL/lymphoma 10			L	IGH@		MALT		1	Insertion - Frameshift(1)	p.I46fs*4(1)	ovary(1)	haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19						c.(136-138)tafs		B-cell CLL/lymphoma 10							83.0	90.0	87.0					1																	85736511		2203	4300	6503	SO:0001589	frameshift_variant	8915				apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding	g.chr1:85736511delT	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.136delA	1.37:g.85736511delT	ENSP00000359612:p.Ile46fs						p.I46fs	NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN		all cancers(265;0.0114)|Epithelial(280;0.0311)	2	873	-			46			CARD.		Q5VUF1	Frame_Shift_Del	DEL	ENST00000370580.1	37	c.136delA	CCDS704.1																																																																																				0.343	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921		17	551						17	551	---	---	---	---
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121116645	121116645	+	lincRNA	DEL	T	T	-	rs377003181		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:121116645delT	ENST00000437515.1	-	0	329					NR_104189.1																						CAAGCCCCCCTTTAAAAAAAA	0.393																																						ENST00000437515.1																			0																																																			0							g.chr1:121116645delT																													1.37:g.121116645delT														0	329	-									RNA	DEL	ENST00000437515.1	37																																																																																						0.393	RP11-343N15.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000098477.2			12	300						12	300	---	---	---	---
LOC101927209	101927209	broad.mit.edu	37	1	142716575	142716578	+	lincRNA	DEL	AAAC	AAAC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:142716575_142716578delAAAC	ENST00000610091.1	-	0	418																											catctcagaaaaacaaacaaacaa	0.422																																						ENST00000595144.1																			0																																																			0							g.chr1:142716575_142716578delAAAC																													1.37:g.142716583_142716586delAAAC														0	418	-									RNA	DEL	ENST00000610091.1	37																																																																																						0.422	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			16	601						16	601	---	---	---	---
MCL1	4170	broad.mit.edu	37	1	150551492	150551494	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:150551492_150551494delTCC	ENST00000369026.2	-	1	572_574	c.513_515delGGA	c.(511-516)gaggac>gac	p.E171del	MCL1_ENST00000464132.1_5'Flank|MCL1_ENST00000307940.3_In_Frame_Del_p.E171del	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		12	587						12	587	---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082957	152082959	+	In_Frame_Del	DEL	CTC	CTC	-	rs143222885	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:152082957_152082959delCTC	ENST00000368804.1	-	2	2733_2735	c.2734_2736delGAG	c.(2734-2736)gagdel	p.E912del		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	912	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCTGTAGCTCCTCCTCCTCC	0.586																																						ENST00000368804.1																			0				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105						c.(2734-2736)del		trichohyalin																																				SO:0001651	inframe_deletion	7062				keratinization	cytoskeleton	calcium ion binding	g.chr1:152082957_152082959delCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2734_2736delGAG	1.37:g.152082966_152082968delCTC	ENSP00000357794:p.Glu912del						p.E912del	NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	2733_2735	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		912			10 X 30 AA tandem repeats.		Q5VUI3	In_Frame_Del	DEL	ENST00000368804.1	37	c.2734_2736delGAG	CCDS41396.1																																																																																				0.586	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		11	1276						11	1276	---	---	---	---
KLHL12	59349	broad.mit.edu	37	1	202862508	202862508	+	Frame_Shift_Del	DEL	C	C	-	rs573767086		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:202862508delC	ENST00000367261.3	-	11	1657	c.1439delG	c.(1438-1440)ggafs	p.G480fs	KLHL12_ENST00000435533.3_Frame_Shift_Del_p.G518fs|KLHL12_ENST00000367259.1_Intron	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	480	Interaction with DVL3.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			ACCATCAAATCCCCCCACCAC	0.453																																						ENST00000367261.3																			0				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14						c.(1438-1440)gafs		kelch-like family member 12							180.0	168.0	172.0					1																	202862508		2203	4300	6503	SO:0001589	frameshift_variant	59349				Wnt receptor signaling pathway		protein binding	g.chr1:202862508delC	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.1439delG	1.37:g.202862508delC	ENSP00000356230:p.Gly480fs					KLHL12_ENST00000435533.3_Frame_Shift_Del_p.G518fs|KLHL12_ENST00000367259.1_Intron	p.G480fs	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	BRCA - Breast invasive adenocarcinoma(75;0.166)		11	1657	-			480			Interaction with DVL3.		A6NEN8|B7Z7B8|Q9HBX5	Frame_Shift_Del	DEL	ENST00000367261.3	37	c.1439delG	CCDS1429.1																																																																																				0.453	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633		7	1159						7	1159	---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214557049	214557051	+	In_Frame_Del	DEL	CCT	CCT	-	rs143136196|rs376331360|rs189081489|rs539310988	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr1:214557049_214557051delCCT	ENST00000366956.5	-	13	2341_2343	c.2147_2149delAGG	c.(2146-2151)gaggct>gct	p.E716del	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	716	Poly-Glu.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.E716delE(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GATTCTGGAGCCTCCTCCTCCTC	0.626																																					Colon(92;557 1424 24372 34121 40073)	ENST00000366956.5																			1	Deletion - In frame(1)	p.E716delE(1)	liver(1)	NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						c.(2146-2151)gct>g		protein tyrosine phosphatase, non-receptor type 14																																				SO:0001651	inframe_deletion	5784				lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding	g.chr1:214557049_214557051delCCT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2147_2149delAGG	1.37:g.214557058_214557060delCCT	ENSP00000355923:p.Glu716del					PTPN14_ENST00000543945.1_3'UTR	p.EA716del	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)	13	2341_2343	-			716			Poly-Glu.		Q5VSI0	In_Frame_Del	DEL	ENST00000366956.5	37	c.2147_2149delAGG	CCDS1514.1																																																																																				0.626	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		15	401						15	401	---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10912688	10912688	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:10912688delA	ENST00000272238.4	+	8	699	c.590delA	c.(589-591)caafs	p.Q197fs	ATP6V1C2_ENST00000381661.3_Frame_Shift_Del_p.Q197fs|RP11-791G15.2_ENST00000606907.1_lincRNA	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	197					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		TCACAATGGCAAAAAACCTAC	0.512																																					NSCLC(188;1042 2136 10807 16813 47705)	ENST00000381661.3																			0				endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						c.(589-591)cafs		ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2							335.0	342.0	340.0					2																	10912688		2203	4300	6503	SO:0001589	frameshift_variant	245973				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain		g.chr2:10912688delA	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.590delA	2.37:g.10912688delA	ENSP00000272238:p.Gln197fs					ATP6V1C2_ENST00000272238.4_Frame_Shift_Del_p.Q197fs	p.Q197fs	NM_144583.3	NP_653184.2	Q8NEY4	VATC2_HUMAN		Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)	8	699	+	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)		197					Q96EL8	Frame_Shift_Del	DEL	ENST00000272238.4	37	c.590delA	CCDS42653.1																																																																																				0.512	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583		7	2755						7	2755	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17898126	17898126	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:17898126delT	ENST00000448223.2	-	14	1497	c.1228delA	c.(1228-1230)atafs	p.I410fs	SMC6_ENST00000402989.1_Frame_Shift_Del_p.I410fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.I410fs|SMC6_ENST00000381272.4_Frame_Shift_Del_p.I436fs	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	410					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AACCAAGATATTTTTTTTTGT	0.343																																						ENST00000448223.2																			0				NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43						c.(1228-1230)tafs		structural maintenance of chromosomes 6							82.0	78.0	80.0					2																	17898126		2203	4297	6500	SO:0001589	frameshift_variant	79677				DNA recombination|DNA repair	chromosome|nucleus	ATP binding	g.chr2:17898126delT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1228delA	2.37:g.17898126delT	ENSP00000404092:p.Ile410fs					SMC6_ENST00000381272.4_Frame_Shift_Del_p.I436fs|SMC6_ENST00000402989.1_Frame_Shift_Del_p.I410fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.I410fs	p.I410fs	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN			14	1497	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)		410					A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Frame_Shift_Del	DEL	ENST00000448223.2	37	c.1228delA	CCDS1690.1																																																																																				0.343	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		10	265						10	265	---	---	---	---
APOB	338	broad.mit.edu	37	2	21228602	21228602	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:21228602delT	ENST00000233242.1	-	26	11265	c.11138delA	c.(11137-11139)aacfs	p.N3713fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3713					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCATTGGGGTTTTTGGTGTA	0.398																																						ENST00000233242.1																			0				NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305						c.(11137-11139)acfs		apolipoprotein B	Atorvastatin(DB01076)						98.0	95.0	96.0					2																	21228602		2203	4300	6503	SO:0001589	frameshift_variant	338				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity	g.chr2:21228602delT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11138delA	2.37:g.21228602delT	ENSP00000233242:p.Asn3713fs						p.N3713fs	NM_000384.2	NP_000375.2	P04114	APOB_HUMAN			26	11265	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		3713					O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	37	c.11138delA	CCDS1703.1																																																																																				0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			7	784						7	784	---	---	---	---
RTN4	57142	broad.mit.edu	37	2	55253745	55253746	+	Frame_Shift_Ins	INS	-	-	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:55253745_55253746insT	ENST00000337526.6	-	3	1732_1733	c.1489_1490insA	c.(1489-1491)atafs	p.I497fs	RTN4_ENST00000357376.3_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.I265fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Frame_Shift_Ins_p.I291fs	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	497					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						CTTTTCTTCTATTTTTTTTTCA	0.381																																						ENST00000337526.6																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						c.(1489-1491)agafs		reticulon 4																																				SO:0001589	frameshift_variant	57142				apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding	g.chr2:55253745_55253746insT	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1490dupA	2.37:g.55253754_55253754dupT	ENSP00000337838:p.Ile497fs					RTN4_ENST00000394611.2_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.R265fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000357376.3_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.R291fs	p.R497fs	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN			3	1732_1733	-			497					O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Frame_Shift_Ins	INS	ENST00000337526.6	37	c.1489_1490insA	CCDS42684.1																																																																																				0.381	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			12	577						12	577	---	---	---	---
HTRA2	27429	broad.mit.edu	37	2	74757185	74757186	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:74757185_74757186insG	ENST00000258080.3	+	1	682_683	c.52_53insG	c.(52-54)cggfs	p.R18fs	AUP1_ENST00000377526.3_5'Flank|HTRA2_ENST00000467961.1_Intron|HTRA2_ENST00000352222.3_Frame_Shift_Ins_p.R18fs	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2	18					adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						TCGGGCATGGCGGGCTTTGGGG	0.718																																						ENST00000258080.3																			0				endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						c.(52-54)ggcfs		HtrA serine peptidase 2																																				SO:0001589	frameshift_variant	27429				apoptosis|proteolysis|response to stress	CD40 receptor complex|endoplasmic reticulum membrane|internal side of plasma membrane|mitochondrial intermembrane space|mitochondrial membrane|nucleus	serine-type endopeptidase activity|unfolded protein binding	g.chr2:74757185_74757186insG		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"""Serine peptidases / Serine peptidases"", ""Parkinson disease"""	14348	protein-coding gene	gene with protein product		606441	"""protease, serine, 25"""	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.55dupG	2.37:g.74757188_74757188dupG	ENSP00000258080:p.Arg18fs					HTRA2_ENST00000352222.3_Frame_Shift_Ins_p.G18fs|HTRA2_ENST00000467961.1_Intron	p.G18fs	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN			1	682_683	+			18					Q9HBZ4|Q9P0Y3|Q9P0Y4	Frame_Shift_Ins	INS	ENST00000258080.3	37	c.52_53insG	CCDS1951.1																																																																																				0.718	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		45	340						45	340	---	---	---	---
AC027612.3	0	broad.mit.edu	37	2	91887905	91887906	+	RNA	INS	-	-	T	rs374250838|rs369805878|rs199562278	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:91887905_91887906insT	ENST00000436174.1	-	0	540																											GCTATTTTCCATTTTTTTTTTT	0.292														393	0.0784744	0.1354	0.0533	5008	,	,		61150	0.0546		0.0567	False		,,,				2504	0.0665					ENST00000436174.1																			0																																																			0							g.chr2:91887905_91887906insT																													2.37:g.91887916_91887916dupT														0	540	-									RNA	INS	ENST00000436174.1	37																																																																																						0.292	AC027612.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000338339.1			12	222						12	222	---	---	---	---
AC027612.3	0	broad.mit.edu	37	2	91899642	91899642	+	RNA	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:91899642delG	ENST00000436174.1	-	0	168																											AAAAAAAAAAGCAAAGTAGGA	0.269																																						ENST00000436174.1																			0																																																			0							g.chr2:91899642delG																													2.37:g.91899642delG														0	168	-									RNA	DEL	ENST00000436174.1	37																																																																																						0.269	AC027612.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000338339.1			8	76						8	76	---	---	---	---
SLC9A4	389015	broad.mit.edu	37	2	103149137	103149137	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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		9	280						9	280	---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109087883	109087884	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:109087883_109087884insA	ENST00000309863.6	+	6	2812_2813	c.2098_2099insA	c.(2098-2100)gaafs	p.E700fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	700					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ACTCAGTTCAGAAAAAAAACAG	0.307																																						ENST00000309863.6																			0				breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						c.(2098-2100)aaafs		GRIP and coiled-coil domain containing 2																																				SO:0001589	frameshift_variant	9648				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding	g.chr2:109087883_109087884insA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2106dupA	2.37:g.109087891_109087891dupA	ENSP00000307939:p.Glu700fs						p.K700fs	NM_181453.3	NP_852118.1	Q8IWJ2	GCC2_HUMAN			6	2812_2813	+			700					A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Ins	INS	ENST00000309863.6	37	c.2098_2099insA	CCDS33268.1																																																																																				0.307	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		11	1483						11	1483	---	---	---	---
TTN	7273	broad.mit.edu	37	2	179459104	179459104	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr2:179459104delA	ENST00000591111.1	-	246	53418	c.53194delT	c.(53194-53196)tgcfs	p.C17732fs	TTN_ENST00000342175.6_Frame_Shift_Del_p.C10500fs|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.C10308fs|TTN_ENST00000359218.5_Frame_Shift_Del_p.C10433fs|TTN_ENST00000342992.6_Frame_Shift_Del_p.C16805fs|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.C19373fs|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17732	Fibronectin type-III 28. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			GGTTTGGTGCAAAATGATGGT	0.373																																						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.(58117-58119)gcfs		titin							112.0	111.0	112.0					2																	179459104		1940	4150	6090	SO:0001589	frameshift_variant	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179459104delA	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.53194delT	2.37:g.179459104delA	ENSP00000465570:p.Cys17732fs					TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.C10308fs|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000591111.1_Frame_Shift_Del_p.C17732fs|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.C16805fs|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.C10500fs|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.C10433fs	p.C19373fs	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)		296	58341	-			17732			Fibronectin type-III 40.		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	Frame_Shift_Del	DEL	ENST00000591111.1	37	c.58117delT																																																																																					0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		9	372						9	372	---	---	---	---
EDEM1	9695	broad.mit.edu	37	3	5248941	5248941	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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		7	657						7	657	---	---	---	---
QRICH1	54870	broad.mit.edu	37	3	49094314	49094316	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:49094314_49094316delTGC	ENST00000395443.2	-	3	1789_1791	c.1317_1319delGCA	c.(1315-1320)cagcaa>caa	p.439_440QQ>Q	QRICH1_ENST00000479449.1_5'UTR|QRICH1_ENST00000424300.1_In_Frame_Del_p.439_440QQ>Q|QRICH1_ENST00000357496.2_In_Frame_Del_p.439_440QQ>Q	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	439	Gln-rich.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		AACTTGGAgttgctgctgctgct	0.562																																						ENST00000395443.2																			0				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25						c.(1315-1320)caa>ca		glutamine-rich 1																																				SO:0001651	inframe_deletion	54870							g.chr3:49094314_49094316delTGC		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1317_1319delGCA	3.37:g.49094323_49094325delTGC	ENSP00000378830:p.Gln440del					QRICH1_ENST00000424300.1_In_Frame_Del_p.QQ439del|QRICH1_ENST00000357496.2_In_Frame_Del_p.QQ439del|QRICH1_ENST00000479449.1_5'UTR	p.QQ439del	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	3	1789_1791	-			439			Gln-rich.		Q4G0F7|Q7L621|Q8TEA5	In_Frame_Del	DEL	ENST00000395443.2	37	c.1317_1319delGCA	CCDS2787.1																																																																																				0.562	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		9	453						9	453	---	---	---	---
PARP3	10039	broad.mit.edu	37	3	51978150	51978152	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:51978150_51978152delAAC	ENST00000417220.2	+	4	717_719	c.229_231delAAC	c.(229-231)aacdel	p.N80del	PARP3_ENST00000431474.1_In_Frame_Del_p.N80del|PARP3_ENST00000398755.3_In_Frame_Del_p.N87del|RRP9_ENST00000232888.6_5'Flank			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	80				N -> K (in Ref. 2; AAD29855). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAACATCGAGAACAACAACAACA	0.596																																						ENST00000417220.2																			0				ovary(1)	1						c.(229-231)del		poly (ADP-ribose) polymerase family, member 3			,	10,3992		5,0,1996					,	-7.6	0.0			201	34,8036		15,4,4016	no	coding,coding	PARP3	NM_005485.4,NM_001003931.2	,	20,4,6012	A1A1,A1R,RR		0.4213,0.2499,0.3645	,	,		44,12028				SO:0001651	inframe_deletion	10039				DNA repair|protein ADP-ribosylation	centriole|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding	g.chr3:51978150_51978152delAAC	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	273	protein-coding gene	gene with protein product	"""poly(ADP-ribose) synthetase-3"", ""NAD+ ADP-ribosyltransferase 3"", ""poly(ADP-ribose) polymerase 3"""	607726	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"""	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.229_231delAAC	3.37:g.51978159_51978161delAAC	ENSP00000395951:p.Asn80del					PARP3_ENST00000431474.1_In_Frame_Del_p.N80del|PARP3_ENST00000398755.3_In_Frame_Del_p.N87del	p.N80del			Q9Y6F1	PARP3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	4	717_719	+			80	N -> K (in Ref. 2; AAD29855).				Q8NER9|Q96CG2|Q9UG81	In_Frame_Del	DEL	ENST00000417220.2	37	c.229_231delAAC	CCDS43097.1																																																																																				0.596	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4		7	1427						7	1427	---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66436625	66436627	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:66436625_66436627delGCT	ENST00000273261.3	-	13	2091_2093	c.1567_1569delAGC	c.(1567-1569)agcdel	p.S524del	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_In_Frame_Del_p.S548del|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	524	Ig-like C2-type 1.|Poly-Ser.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TCATGGGGGAGCTGCTGCTGCTG	0.547																																						ENST00000383703.3																			0				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42						c.(1639-1641)del		leucine-rich repeats and immunoglobulin-like domains 1																																				SO:0001651	inframe_deletion	26018					integral to membrane		g.chr3:66436625_66436627delGCT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1567_1569delAGC	3.37:g.66436634_66436636delGCT	ENSP00000273261:p.Ser524del					LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000273261.3_In_Frame_Del_p.S524del|SLC25A26_ENST00000536651.1_3'UTR	p.S548del			Q96JA1	LRIG1_HUMAN		BRCA - Breast invasive adenocarcinoma(55;0.00047)	14	2242_2244	-		Lung NSC(201;0.0101)	524			Ig-like C2-type 1.		Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	In_Frame_Del	DEL	ENST00000273261.3	37	c.1639_1641delAGC	CCDS33783.1																																																																																				0.547	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		8	1609						8	1609	---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113286403	113286403	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:113286403delA	ENST00000264852.4	+	3	1087	c.361delA	c.(361-363)aacfs	p.N121fs	SIDT1_ENST00000393830.3_Frame_Shift_Del_p.N121fs	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	121					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GAGGAGCTACAACTATCAAGA	0.468																																						ENST00000264852.4																			0				breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						c.(361-363)acfs		SID1 transmembrane family, member 1							85.0	79.0	81.0					3																	113286403		2203	4300	6503	SO:0001589	frameshift_variant	54847					integral to membrane		g.chr3:113286403delA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.361delA	3.37:g.113286403delA	ENSP00000264852:p.Asn121fs					SIDT1_ENST00000393830.3_Frame_Shift_Del_p.N121fs	p.N121fs	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN			3	1087	+			121					Q17RR4	Frame_Shift_Del	DEL	ENST00000264852.4	37	c.361delA	CCDS2974.1																																																																																				0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		20	547						20	547	---	---	---	---
ATR	545	broad.mit.edu	37	3	142241646	142241648	+	In_Frame_Del	DEL	AAT	AAT	-	rs562594343		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:142241646_142241648delAAT	ENST00000350721.4	-	23	4309_4311	c.4188_4190delATT	c.(4186-4191)ttattg>ttg	p.1396_1397LL>L	ATR_ENST00000383101.3_In_Frame_Del_p.1332_1333LL>L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1396					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TAGCTCCATCAATAATCCATAGG	0.379								Other conserved DNA damage response genes																														ENST00000350721.4																			0				NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						c.(4186-4191)ttg>tt	Other conserved DNA damage response genes	ataxia telangiectasia and Rad3 related																																				SO:0001651	inframe_deletion	545				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity	g.chr3:142241646_142241648delAAT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4188_4190delATT	3.37:g.142241649_142241651delAAT	ENSP00000343741:p.Leu1397del					ATR_ENST00000383101.3_In_Frame_Del_p.LL1332del	p.LL1396del	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN			23	4309_4311	-			1396					Q59HB2|Q7KYL3|Q93051|Q9BXK4	In_Frame_Del	DEL	ENST00000350721.4	37	c.4188_4190delATT	CCDS3124.1																																																																																				0.379	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		12	571						12	571	---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149260194	149260196	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr3:149260194_149260196delCTG	ENST00000465804.1	-	5	953_955	c.697_699delCAG	c.(697-699)cagdel	p.Q233del	WWTR1_ENST00000467467.1_In_Frame_Del_p.Q233del|WWTR1_ENST00000360632.3_In_Frame_Del_p.Q233del	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	233	Gln-rich.				cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GCCGCAGTTTCTGCTGCTGCTGC	0.581			T	CAMTA1	epitheliod hemangioendothelioma																																	ENST00000465804.1				Dom	yes		3	3q23-q24	607392	T	WW domain containing transcription regulator 1			M	CAMTA1		epitheliod hemangioendothelioma		0				breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23						c.(697-699)del		WW domain containing transcription regulator 1																																				SO:0001651	inframe_deletion	25937				hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity	g.chr3:149260194_149260196delCTG	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.697_699delCAG	3.37:g.149260203_149260205delCTG	ENSP00000419465:p.Gln233del					WWTR1_ENST00000360632.3_In_Frame_Del_p.Q233del|WWTR1_ENST00000467467.1_In_Frame_Del_p.Q233del	p.Q233del	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)		5	953_955	-			233			Gln-rich.		D3DNH7|Q8N3P2|Q9Y3W6	In_Frame_Del	DEL	ENST00000465804.1	37	c.697_699delCAG	CCDS3144.1																																																																																				0.581	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		8	349						8	349	---	---	---	---
ZNF876P	642280	broad.mit.edu	37	4	212236	212236	+	RNA	DEL	A	A	-	rs80061878		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:212236delA	ENST00000356347.3	+	0	172					NR_027481.1		Q49A33	Z876P_HUMAN	zinc finger protein 876, pseudogene						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										ctaaaaatacaaaaaaaaaaa	0.493																																						ENST00000356347.3																			0																																																			0							g.chr4:212236delA	BC028359		4p16.3	2011-04-20	2010-08-03	2009-07-22	ENSG00000198155	ENSG00000198155			32472	pseudogene	pseudogene							Standard	NR_027481		Approved		uc010iba.4	Q49A33	OTTHUMG00000159874		4.37:g.212236delA								NR_027481.1						0	172	+									RNA	DEL	ENST00000356347.3	37																																																																																						0.493	ZNF876P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357870.2	NR_027481		7	10						7	10	---	---	---	---
GABRG1	2565	broad.mit.edu	37	4	46060358	46060358	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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		9	376						9	376	---	---	---	---
PKD2	5311	broad.mit.edu	37	4	88986559	88986559	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:88986559delA	ENST00000508588.1	+	6	801	c.406delA	c.(406-408)aaafs	p.K137fs	PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000237596.2_Frame_Shift_Del_p.K719fs			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	389					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		ACTAAAACTGAAAAAAAATAC	0.383																																						ENST00000237596.2																			0				breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36						c.(2152-2154)aafs		polycystic kidney disease 2 (autosomal dominant)							102.0	109.0	106.0					4																	88986559		2203	4300	6503	SO:0001589	frameshift_variant	5311					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity	g.chr4:88986559delA	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.406delA	4.37:g.88986559delA	ENSP00000427131:p.Lys137fs					PKD2_ENST00000502363.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000508588.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000511337.1_3'UTR	p.K719fs	NM_000297.3	NP_000288.1	Q13563	PKD2_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)	11	2218	+		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)	719			EF-hand domain.		Q8TB08|Q9P0T6|Q9Y3X8	Frame_Shift_Del	DEL	ENST00000508588.1	37	c.2152delA																																																																																					0.383	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		9	752						9	752	---	---	---	---
NAP1L5	266812	broad.mit.edu	37	4	89618484	89618486	+	In_Frame_Del	DEL	TCC	TCC	-	rs201095744|rs147461195	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:89618484_89618486delTCC	ENST00000323061.5	-	1	900_902	c.420_422delGGA	c.(418-423)gaggaa>gaa	p.140_141EE>E	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	140	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		gtactcctcttcctcctcctcct	0.606														5	0.000998403	0.0008	0.0058	5008	,	,		14727	0.0		0.0	False		,,,				2504	0.0					ENST00000323061.5																			0				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7						c.(418-423)gaa>ga		nucleosome assembly protein 1-like 5																																				SO:0001651	inframe_deletion	266812				nucleosome assembly	nucleus	protein binding	g.chr4:89618484_89618486delTCC	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.420_422delGGA	4.37:g.89618493_89618495delTCC	ENSP00000320488:p.Glu143del					HERC3_ENST00000402738.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000543130.1_Intron	p.EE142del	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000181)	1	900_902	-			142			Glu-rich.			In_Frame_Del	DEL	ENST00000323061.5	37	c.420_422delGGA	CCDS3632.1																																																																																				0.606	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757		17	459						17	459	---	---	---	---
OTUD4	54726	broad.mit.edu	37	4	146077123	146077125	+	In_Frame_Del	DEL	CAG	CAG	-	rs150581210		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr4:146077123_146077125delCAG	ENST00000447906.2	-	8	840_842	c.653_655delCTG	c.(652-657)gctgat>gat	p.A218del	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_In_Frame_Del_p.A153del			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	218					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					CCATTCACATCAGCAGCAGCAGC	0.34																																						ENST00000454497.2																			0				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						c.(457-462)gat>g		OTU domain containing 4																																				SO:0001651	inframe_deletion	54726						protein binding	g.chr4:146077123_146077125delCAG		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.653_655delCTG	4.37:g.146077132_146077134delCAG	ENSP00000395487:p.Ala218del					OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000447906.2_In_Frame_Del_p.AD218del	p.AD153del	NM_001102653.1	NP_001096123.1	Q01804	OTUD4_HUMAN			8	595_597	-	all_hematologic(180;0.151)		218			OTU.		B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	In_Frame_Del	DEL	ENST00000447906.2	37	c.458_460delCTG																																																																																					0.340	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		7	427						7	427	---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24492973	24492973	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:24492973delA	ENST00000264463.4	-	10	2084	c.1577delT	c.(1576-1578)ttcfs	p.F526fs	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	526	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AGCTAAACTGAAAAAAAATTT	0.313										HNSCC(23;0.051)																												ENST00000264463.4																			0				NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185						c.(1576-1578)tcfs		cadherin 10, type 2 (T2-cadherin)							170.0	183.0	179.0					5																	24492973		2203	4298	6501	SO:0001589	frameshift_variant	1008				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:24492973delA	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1577delT	5.37:g.24492973delA	ENSP00000264463:p.Phe526fs	HNSCC(23;0.051)				CDH10_ENST00000502921.1_5'UTR	p.F526fs	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN		STAD - Stomach adenocarcinoma(35;0.0556)	10	2084	-			526			Cadherin 5.		Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	37	c.1577delT	CCDS3892.1																																																																																				0.313	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		7	967						7	967	---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32419951	32419953	+	In_Frame_Del	DEL	GGT	GGT	-	rs376016449		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:32419951_32419953delGGT	ENST00000265069.8	-	3	495_497	c.393_395delACC	c.(391-396)ccaccc>ccc	p.131_132PP>P		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	131	Ala-rich.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AGTAGCTGGGGGTGGTGGTGGTG	0.483																																						ENST00000265069.8																			0				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32						c.(391-396)ccc>cc		zinc finger RNA binding protein																																				SO:0001651	inframe_deletion	51663				multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding	g.chr5:32419951_32419953delGGT	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.393_395delACC	5.37:g.32419960_32419962delGGT	ENSP00000265069:p.Pro133del						p.PP131del	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN		STAD - Stomach adenocarcinoma(35;0.19)	3	495_497	-			131			Ala-rich.		B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	In_Frame_Del	DEL	ENST00000265069.8	37	c.393_395delACC	CCDS34139.1																																																																																				0.483	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			8	1076						8	1076	---	---	---	---
C1QTNF3	114899	broad.mit.edu	37	5	34042955	34042955	+	Intron	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:34042955delT	ENST00000231338.7	-	1	172				RP11-1084J3.4_ENST00000382079.3_Intron|C1QTNF3_ENST00000382065.3_Frame_Shift_Del_p.L92fs	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3						cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					TGATCTGGGCTAGGTCATCTA	0.453																																						ENST00000382065.3																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17						c.(274-276)ctfs		C1q and tumor necrosis factor related protein 3			,	0,4266		0,0,2133	103.0	107.0	106.0		,	5.6	1.0	5		104	2,8252		0,2,4125	no	frameshift,intron	C1QTNF3	NM_181435.5,NM_030945.3	,	0,2,6258	A1A1,A1R,RR		0.0242,0.0,0.016	,	,	34042955	2,12518	2203	4300	6503	SO:0001627	intron_variant	114899					collagen		g.chr5:34042955delT	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"""cartonectin"""	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.84+191A>-	5.37:g.34042955delT						C1QTNF3_ENST00000231338.7_Intron	p.L92fs	NM_181435.5	NP_852100.3	Q9BXJ4	C1QT3_HUMAN			1	982	-	all_lung(31;0.0207)		0			Collagen-like.		Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Frame_Shift_Del	DEL	ENST00000231338.7	37	c.276delA	CCDS3904.1																																																																																				0.453	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	NM_030945		15	872						15	872	---	---	---	---
FGF10	2255	broad.mit.edu	37	5	44388715	44388717	+	In_Frame_Del	DEL	AGC	AGC	-	rs576181814		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:44388715_44388717delAGC	ENST00000264664.4	-	1	182_184	c.68_70delGCT	c.(67-72)tgcttt>ttt	p.C23del	RP11-473L15.2_ENST00000502457.1_RNA	NM_004465.1	NP_004456.1	O15520	FGF10_HUMAN	fibroblast growth factor 10	23					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchiole morphogenesis (GO:0060436)|bud elongation involved in lung branching (GO:0060449)|bud outgrowth involved in lung branching (GO:0060447)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell migration (GO:0010631)|epithelial cell proliferation (GO:0050673)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|ERK1 and ERK2 cascade (GO:0070371)|establishment of mitotic spindle orientation (GO:0000132)|Fc-epsilon receptor signaling pathway (GO:0038095)|female genitalia morphogenesis (GO:0048807)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|hair follicle morphogenesis (GO:0031069)|Harderian gland development (GO:0070384)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte proliferation (GO:0043616)|lacrimal gland development (GO:0032808)|limb bud formation (GO:0060174)|lung epithelium development (GO:0060428)|lung proximal/distal axis specification (GO:0061115)|lung saccule development (GO:0060430)|male genitalia morphogenesis (GO:0048808)|mammary gland bud formation (GO:0060615)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal-epithelial cell signaling involved in lung development (GO:0060496)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|metanephros morphogenesis (GO:0003338)|muscle cell fate commitment (GO:0042693)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|pancreas development (GO:0031016)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of ATPase activity (GO:0032781)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urothelial cell proliferation (GO:0050677)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of white fat cell proliferation (GO:0070352)|prostatic bud formation (GO:0060513)|protein localization to cell surface (GO:0034394)|radial glial cell differentiation (GO:0060019)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of saliva secretion (GO:0046877)|regulation of smoothened signaling pathway (GO:0008589)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|salivary gland development (GO:0007431)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|semicircular canal fusion (GO:0060879)|smooth muscle cell differentiation (GO:0051145)|somatic stem cell maintenance (GO:0035019)|spleen development (GO:0048536)|submandibular salivary gland formation (GO:0060661)|tear secretion (GO:0070075)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tissue regeneration (GO:0042246)|Type II pneumocyte differentiation (GO:0060510)|urothelial cell proliferation (GO:0050674)|white fat cell differentiation (GO:0050872)|wound healing (GO:0042060)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chemoattractant activity (GO:0042056)|fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|type 2 fibroblast growth factor receptor binding (GO:0005111)			haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1)	13	Lung NSC(6;1.12e-06)					AGCAACAAAAAGCAGCAGCAGCA	0.537																																						ENST00000264664.4																			0				haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1)	13						c.(67-72)ttt>t		fibroblast growth factor 10																																				SO:0001651	inframe_deletion	2255				actin cytoskeleton reorganization|activation of MAPK activity|bud outgrowth involved in lung branching|ERK1 and ERK2 cascade|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|insulin receptor signaling pathway|lacrimal gland development|lung saccule development|mesonephros development|negative regulation of cell cycle arrest|positive regulation of ATPase activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of DNA repair|positive regulation of DNA replication|positive regulation of epithelial cell migration|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of ERK1 and ERK2 cascade|positive regulation of hair follicle cell proliferation|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of lymphocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of urothelial cell proliferation|protein localization at cell surface|radial glial cell differentiation|regulation of saliva secretion|response to protein stimulus|secretion by lung epithelial cell involved in lung growth|tear secretion|thymus development|urothelial cell proliferation	cell surface|extracellular space|nucleus|plasma membrane	chemoattractant activity|growth factor activity|heparin binding|type 2 fibroblast growth factor receptor binding	g.chr5:44388715_44388717delAGC		CCDS3950.1	5p13-p12	2008-02-05			ENSG00000070193	ENSG00000070193			3666	protein-coding gene	gene with protein product		602115				9287324	Standard	NM_004465		Approved		uc003jog.1	O15520	OTTHUMG00000131153	ENST00000264664.4:c.68_70delGCT	5.37:g.44388724_44388726delAGC	ENSP00000264664:p.Cys23del						p.CF23del	NM_004465.1	NP_004456.1	O15520	FGF10_HUMAN			1	182_184	-	Lung NSC(6;1.12e-06)		23					C7FDY0|Q6FHR3|Q6FHT6|Q96P59	In_Frame_Del	DEL	ENST00000264664.4	37	c.68_70delGCT	CCDS3950.1																																																																																				0.537	FGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253845.2	NM_004465		7	423						7	423	---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69730714	69730715	+	RNA	INS	-	-	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:69730714_69730715insT	ENST00000513202.1	+	0	753					NR_033417.1				general transcription factor IIH, polypeptide 2B (pseudogene)																		CTATGAAGGTGTTTTTTTTTCC	0.322																																						ENST00000513202.1																			0																	31,3641		1,29,1806						1.3	0.0			103	24,7012		0,24,3494	no	intergenic				1,53,5300	A1A1,A1R,RR		0.3411,0.8442,0.5136				55,10653						0							g.chr5:69730714_69730715insT			5q13.2	2011-09-01	2011-09-01		ENSG00000226259	ENSG00000226259		"""General transcription factors"""	31393	pseudogene	pseudogene			"""general transcription factor IIH, polypeptide 2B"""				Standard	NR_033417		Approved	DKFZP686M0199	uc021yab.1		OTTHUMG00000162394		5.37:g.69730723_69730723dupT								NR_033417.1						0	753	+									RNA	INS	ENST00000513202.1	37																																																																																						0.322	GTF2H2B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000396209.1	NM_001098729		13	479						13	479	---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79372774	79372776	+	In_Frame_Del	DEL	TGA	TGA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:79372774_79372776delTGA	ENST00000350881.2	+	16	2179_2181	c.1989_1991delTGA	c.(1987-1992)tgtgat>tgt	p.D668del	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_In_Frame_Del_p.D577del|CTD-2201I18.1_ENST00000514042.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	668					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GTGACGAGTGTGATGATGATGAT	0.562																																						ENST00000350881.2																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34						c.(1987-1992)tgt>tg		thrombospondin 4																																				SO:0001651	inframe_deletion	7060				endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity	g.chr5:79372774_79372776delTGA		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.1989_1991delTGA	5.37:g.79372783_79372785delTGA	ENSP00000339730:p.Asp668del					CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_RNA|THBS4_ENST00000511733.1_In_Frame_Del_p.CD572del	p.CD663del	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)	16	2179_2181	+		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)	663					B2R909|Q86TG2	In_Frame_Del	DEL	ENST00000350881.2	37	c.1989_1991delTGA	CCDS4049.1																																																																																				0.562	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			9	1531						9	1531	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79970915	79970915	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:79970915delA	ENST00000265081.6	+	7	1221	c.1141delA	c.(1141-1143)aaafs	p.K383fs		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	383					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TGTTAGGGACAAAAAAAAGGG	0.348								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(1141-1143)aafs	Mismatch excision repair (MMR)	mutS homolog 3							142.0	146.0	144.0					5																	79970915		2203	4300	6503	SO:0001589	frameshift_variant	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79970915delA	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1141delA	5.37:g.79970915delA	ENSP00000265081:p.Lys383fs						p.K383fs	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	7	1221	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	383					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Del	DEL	ENST00000265081.6	37	c.1141delA	CCDS34195.1																																																																																				0.348	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		12	892						12	892	---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122881495	122881495	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:122881495delA	ENST00000361991.2	+	1	168	c.138delA	c.(136-138)ggafs	p.G46fs	CSNK1G3_ENST00000345990.4_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000395412.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000512718.3_Intron|CSNK1G3_ENST00000360683.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000510842.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000395411.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000508708.1_3'UTR|CSNK1G3_ENST00000521364.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000511130.2_Intron			Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1)	15		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		TTAGAGTTGGAAAAAAAATTG	0.363																																					Pancreas(187;2868 2964 4353 6297)	ENST00000395412.1																			0				autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1)	15						c.(136-138)ggfs		casein kinase 1, gamma 3							102.0	101.0	101.0					5																	122881495		2203	4300	6503	SO:0001589	frameshift_variant	1456				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity	g.chr5:122881495delA	AF049090	CCDS4135.1, CCDS34218.1, CCDS43355.1, CCDS59491.1, CCDS59492.1, CCDS59493.1	5q23	2013-01-17			ENSG00000151292	ENSG00000151292			2456	protein-coding gene	gene with protein product		604253				9925945	Standard	NM_004384		Approved		uc031skv.1	Q9Y6M4	OTTHUMG00000128923	ENST00000361991.2:c.138delA	5.37:g.122881495delA	ENSP00000354942:p.Gly46fs					CSNK1G3_ENST00000361991.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000360683.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000512718.3_Intron|CSNK1G3_ENST00000521364.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000345990.4_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000508708.1_3'UTR|CSNK1G3_ENST00000511130.2_Intron|CSNK1G3_ENST00000510842.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000395411.1_Frame_Shift_Del_p.G46fs	p.G46fs	NM_001044723.1	NP_001038188.1	Q9Y6M4	KC1G3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)	2	857	+		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	46			Protein kinase.		A8K040|B4DSH2|B7Z9Q4|E7EVD0|Q86WZ7|Q9Y6M3	Frame_Shift_Del	DEL	ENST00000361991.2	37	c.138delA	CCDS4135.1																																																																																				0.363	CSNK1G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250900.1	NM_004384		8	737						8	737	---	---	---	---
ANKHD1	54882	broad.mit.edu	37	5	139905676	139905676	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:139905676delA	ENST00000360839.2	+	26	4742	c.4588delA	c.(4588-4590)aaafs	p.K1531fs	SNORD45_ENST00000363181.1_RNA|ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.K1531fs|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1531fs|ANKHD1_ENST00000544120.1_5'Flank	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		9	1146						9	1146	---	---	---	---
PCDHB14	56122	broad.mit.edu	37	5	140604247	140604247	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:140604247delT	ENST00000239449.4	+	1	1170	c.1170delT	c.(1168-1170)cctfs	p.P390fs	PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.P237fs	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	390	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATAACCTCCCTTTTTTCCTGA	0.443																																					Ovarian(141;50 1831 27899 33809 37648)	ENST00000239449.4																			0				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49						c.(1168-1170)ccfs									116.0	120.0	118.0					5																	140604247		2203	4300	6503	SO:0001589	frameshift_variant	0				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140604247delT	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1170delT	5.37:g.140604247delT	ENSP00000239449:p.Pro390fs					PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.P237fs	p.P390fs	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	1170	+			390			Cadherin 4.		B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	37	c.1170delT	CCDS4256.1																																																																																				0.443	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		7	893						7	893	---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145647320	145647320	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:145647320delA	ENST00000265271.5	+	15	2606	c.2440delA	c.(2440-2442)aaafs	p.K816fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.K761fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	816					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K816fs*5(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAAGTGCTTAAAAAAAAACA	0.348																																						ENST00000265271.5																			1	Deletion - Frameshift(1)	p.K816fs*5(1)	ovary(1)	NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39						c.(2440-2442)aafs		RNA binding motif protein 27							79.0	73.0	75.0					5																	145647320		1568	3582	5150	SO:0001589	frameshift_variant	54439				mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding	g.chr5:145647320delA	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2440delA	5.37:g.145647320delA	ENSP00000265271:p.Lys816fs					RBM27_ENST00000506502.1_Frame_Shift_Del_p.K761fs	p.K816fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		15	2606	+			816					Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	37	c.2440delA	CCDS43378.1																																																																																				0.348	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		9	407						9	407	---	---	---	---
PPARGC1B	133522	broad.mit.edu	37	5	149216457	149216459	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:149216457_149216459delGGA	ENST00000309241.5	+	8	2471_2473	c.2439_2441delGGA	c.(2437-2442)ggggag>ggg	p.E818del	PPARGC1B_ENST00000403750.1_In_Frame_Del_p.E754del|PPARGC1B_ENST00000394320.3_In_Frame_Del_p.E818del|PPARGC1B_ENST00000360453.4_In_Frame_Del_p.E779del	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	818	Glu-rich.				actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			aggaagaaggggaggaggaggag	0.606																																						ENST00000309241.5																			0				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30						c.(2437-2442)ggg>gg		peroxisome proliferator-activated receptor gamma, coactivator 1 beta																																				SO:0001651	inframe_deletion	133522				estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity	g.chr5:149216457_149216459delGGA	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2439_2441delGGA	5.37:g.149216466_149216468delGGA	ENSP00000312649:p.Glu818del					PPARGC1B_ENST00000403750.1_In_Frame_Del_p.GE749del|PPARGC1B_ENST00000360453.4_In_Frame_Del_p.GE774del|PPARGC1B_ENST00000394320.3_In_Frame_Del_p.GE813del	p.GE813del	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		8	2471_2473	+			813			Glu-rich.		A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	In_Frame_Del	DEL	ENST00000309241.5	37	c.2439_2441delGGA	CCDS4298.1																																																																																				0.606	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		8	580						8	580	---	---	---	---
STK10	6793	broad.mit.edu	37	5	171583751	171583760	+	Frame_Shift_Del	DEL	GACTTTGGCC	GACTTTGGCC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr5:171583751_171583760delGACTTTGGCC	ENST00000176763.5	-	2	532_541	c.189_198delGGCCAAAGTC	c.(187-198)gcggccaaagtcfs	p.AAKV63fs		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	63	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGTTTCAATGACTTTGGCCGCAGCCAAAG	0.552																																						ENST00000176763.5																			0				breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47						c.(187-198)gcfs		serine/threonine kinase 10																																				SO:0001589	frameshift_variant	6793						ATP binding|protein serine/threonine kinase activity	g.chr5:171583751_171583760delGACTTTGGCC	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.189_198delGGCCAAAGTC	5.37:g.171583751_171583760delGACTTTGGCC	ENSP00000176763:p.Ala63fs						p.AAKV63fs	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		2	532_541	-	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	63			Protein kinase.		A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Frame_Shift_Del	DEL	ENST00000176763.5	37	c.189_198delGGCCAAAGTC	CCDS34290.1																																																																																				0.552	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		15	728						15	728	---	---	---	---
EDN1	1906	broad.mit.edu	37	6	12292614	12292615	+	Frame_Shift_Ins	INS	-	-	G	rs183694577	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:12292614_12292615insG	ENST00000379375.5	+	2	372_373	c.105_106insG	c.(106-108)gggfs	p.G36fs		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	36					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				GTGAGAACGGCGGGGAGAAACC	0.619																																						ENST00000379375.5																			0				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	GRCh37	CM076165	EDN1	M	rs183694577	c.(103-108)gggggafs		endothelin 1																																				SO:0001589	frameshift_variant	1906				artery smooth muscle contraction|calcium-mediated signaling|leukocyte activation|negative regulation of blood coagulation|negative regulation of cellular protein metabolic process|negative regulation of nitric-oxide synthase biosynthetic process|negative regulation of transcription from RNA polymerase II promoter|nitric oxide transport|peptide hormone secretion|phosphatidylinositol 3-kinase cascade|positive regulation of cardiac muscle hypertrophy|positive regulation of cell size|positive regulation of endothelial cell migration|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of JUN kinase activity|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of sarcomere organization|positive regulation of smooth muscle cell proliferation|prostaglandin biosynthetic process|protein kinase C deactivation|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	cytoplasm|extracellular space	cytokine activity|endothelin A receptor binding|endothelin B receptor binding|hormone activity	g.chr6:12292614_12292615insG	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.109dupG	6.37:g.12292618_12292618dupG	ENSP00000368683:p.Gly36fs						p.GG35fs	NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN			2	372_373	+	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)	35					Q96DA1	Frame_Shift_Ins	INS	ENST00000379375.5	37	c.105_106insG	CCDS4522.1																																																																																				0.619	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955		7	765						7	765	---	---	---	---
HIST1H4K	8362	broad.mit.edu	37	6	27799162	27799163	+	Frame_Shift_Ins	INS	-	-	A	rs544620282	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:27799162_27799163insA	ENST00000357549.2	-	1	142_143	c.143_144insT	c.(142-144)tccfs	p.S48fs		NM_003541.2	NP_003532.1	P62805	H4_HUMAN	histone cluster 1, H4k	48					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)	7						AGATGAGGCCGGAGATGCGCTT	0.644													-|-|A|insertion	3	0.000599042	0.0	0.0	5008	,	,		17577	0.0		0.003	False		,,,				2504	0.0					ENST00000357549.2																			0				breast(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)	7						c.(142-144)tggfs		histone cluster 1, H4k				0,3570		0,0,1785						-8.4	0.5			7	17,7413		3,11,3701	no	frameshift	HIST1H4K	NM_003541.2		3,11,5486	A1A1,A1R,RR		0.2288,0.0,0.1545				17,10983				SO:0001589	frameshift_variant	8362				CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding	g.chr6:27799162_27799163insA	X60483	CCDS4631.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197914	ENSG00000273542		"""Histones / Replication-dependent"""	4784	protein-coding gene	gene with protein product		602825	"""H4 histone family, member D"", ""histone 1, H4k"""	H4FD		9439656, 12408966	Standard	NM_003541		Approved	H4/d, H4F2iii, dJ160A22.1	uc003njr.3	P62805	OTTHUMG00000014488	ENST00000357549.2:c.143_144insT	6.37:g.27799162_27799163insA	ENSP00000350159:p.Ser48fs						p.W48fs	NM_003541.2	NP_003532.1	P62805	H4_HUMAN			1	142_143	-			48					A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Frame_Shift_Ins	INS	ENST00000357549.2	37	c.143_144insT	CCDS4631.1																																																																																				0.644	HIST1H4K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040156.1	NM_003541		7	192						7	192	---	---	---	---
OR2J2	26707	broad.mit.edu	37	6	29141422	29141422	+	Frame_Shift_Del	DEL	A	A	-	rs556940268|rs201438710	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:29141422delA	ENST00000377167.2	+	1	112	c.10delA	c.(10-12)aaafs	p.K5fs		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						AATGATGATTAAAAAAAATGC	0.358													AAAAAAAA|AAAAAAAA|AAAAAAA|deletion	21	0.00419329	0.0144	0.0014	5008	,	,		19015	0.0		0.001	False		,,,				2504	0.0					ENST00000377167.2																			0				endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						c.(10-12)aafs		olfactory receptor, family 2, subfamily J, member 2							105.0	102.0	103.0					6																	29141422		1836	4079	5915	SO:0001589	frameshift_variant	26707				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr6:29141422delA		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.10delA	6.37:g.29141422delA	ENSP00000366372:p.Lys5fs						p.K5fs	NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN			1	112	+			5					A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Frame_Shift_Del	DEL	ENST00000377167.2	37	c.10delA	CCDS43434.1																																																																																				0.358	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			8	634						8	634	---	---	---	---
PPP1R10	5514	broad.mit.edu	37	6	30570264	30570266	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:30570264_30570266delGGA	ENST00000376511.2	-	19	2712_2714	c.2160_2162delTCC	c.(2158-2163)cctcca>cca	p.720_721PP>P		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	720	Gly-rich.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GCCTCGGAATggaggaggaggag	0.67																																						ENST00000376511.2																			0				cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						c.(2158-2163)cca>cc		protein phosphatase 1, regulatory subunit 10				21,3195		2,17,1589						-7.6	0.5			35	55,6059		6,43,3008	no	coding	PPP1R10	NM_002714.2		8,60,4597	A1A1,A1R,RR		0.8996,0.653,0.8146				76,9254				SO:0001651	inframe_deletion	5514				protein import into nucleus|transcription, DNA-dependent	PTW/PP1 phosphatase complex	DNA binding|protein phosphatase inhibitor activity|RNA binding|zinc ion binding	g.chr6:30570264_30570266delGGA	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9284	protein-coding gene	gene with protein product	"""phosphatase 1 nuclear targeting subunit"", ""HLA-C associated transcript 53"""	603771	"""protein phosphatase 1, regulatory (inhibitor) subunit 10"""			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.2160_2162delTCC	6.37:g.30570273_30570275delGGA	ENSP00000365694:p.Pro721del						p.PP720del	NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN			19	2712_2714	-			720			Gly-rich.		O00405	In_Frame_Del	DEL	ENST00000376511.2	37	c.2160_2162delTCC	CCDS4681.1																																																																																				0.670	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		7	390						7	390	---	---	---	---
STK19	8859	broad.mit.edu	37	6	31939825	31939826	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:31939825_31939826insG	ENST00000375333.2	+	1	105_106	c.52_53insG	c.(52-54)cggfs	p.R18fs	STK19_ENST00000375331.2_Frame_Shift_Ins_p.R18fs|DXO_ENST00000375356.3_5'Flank|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375349.3_5'UTR|DXO_ENST00000337523.5_5'UTR	NM_032454.1	NP_115830.1	P49842	STK19_HUMAN	serine/threonine kinase 19	18					protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			skin(5)|upper_aerodigestive_tract(2)	7						GCGACAGTGGCGGGCAAACCCC	0.634																																						ENST00000375331.2																			0				skin(5)|upper_aerodigestive_tract(2)	7						c.(52-54)ggcfs		serine/threonine kinase 19																																				SO:0001589	frameshift_variant	8859					nucleus	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr6:31939825_31939826insG	X77474	CCDS4733.1, CCDS34417.1	6p21.33	2011-09-15			ENSG00000204344	ENSG00000204344			11398	protein-coding gene	gene with protein product		604977				8012361, 9812991	Standard	NM_032454		Approved	D6S60, G11, RP1	uc003nyv.3	P49842	OTTHUMG00000166424	ENST00000375333.2:c.55dupG	6.37:g.31939828_31939828dupG	ENSP00000364482:p.Arg18fs					STK19_ENST00000375333.2_Frame_Shift_Ins_p.G18fs|DOM3Z_ENST00000375349.3_5'UTR|DOM3Z_ENST00000478221.1_5'UTR|DOM3Z_ENST00000337523.5_5'UTR	p.G18fs	NM_004197.1	NP_004188.1	P49842	STK19_HUMAN			1	218_219	+			18					A6NF95|A6NFW8|B0QZR5|Q13159|Q31617|Q5JP77|Q5ST72|Q5ST75	Frame_Shift_Ins	INS	ENST00000375333.2	37	c.52_53insG	CCDS4733.1																																																																																				0.634	STK19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076484.3			31	907						31	907	---	---	---	---
STK19	8859	broad.mit.edu	37	6	31939829	31939830	+	Frame_Shift_Ins	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:31939829_31939830insA	ENST00000375333.2	+	1	109_110	c.56_57insA	c.(55-60)gcaaacfs	p.N20fs	STK19_ENST00000375331.2_Frame_Shift_Ins_p.N20fs|DXO_ENST00000375356.3_5'Flank|DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375349.3_5'UTR|DXO_ENST00000337523.5_5'UTR	NM_032454.1	NP_115830.1	P49842	STK19_HUMAN	serine/threonine kinase 19	20					protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			skin(5)|upper_aerodigestive_tract(2)	7						CAGTGGCGGGCAAACCCCTCCC	0.634																																						ENST00000375331.2																			0				skin(5)|upper_aerodigestive_tract(2)	7						c.(55-57)gaafs		serine/threonine kinase 19																																				SO:0001589	frameshift_variant	8859					nucleus	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr6:31939829_31939830insA	X77474	CCDS4733.1, CCDS34417.1	6p21.33	2011-09-15			ENSG00000204344	ENSG00000204344			11398	protein-coding gene	gene with protein product		604977				8012361, 9812991	Standard	NM_032454		Approved	D6S60, G11, RP1	uc003nyv.3	P49842	OTTHUMG00000166424	ENST00000375333.2:c.59dupA	6.37:g.31939832_31939832dupA	ENSP00000364482:p.Asn20fs					STK19_ENST00000375333.2_Frame_Shift_Ins_p.E19fs|DOM3Z_ENST00000375349.3_5'UTR|DOM3Z_ENST00000478221.1_5'UTR|DOM3Z_ENST00000337523.5_5'UTR	p.E19fs	NM_004197.1	NP_004188.1	P49842	STK19_HUMAN			1	222_223	+			19					A6NF95|A6NFW8|B0QZR5|Q13159|Q31617|Q5JP77|Q5ST72|Q5ST75	Frame_Shift_Ins	INS	ENST00000375333.2	37	c.56_57insA	CCDS4733.1																																																																																				0.634	STK19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076484.3			16	780						16	780	---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34804004	34804006	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:34804004_34804006delCAG	ENST00000192788.5	+	8	1083_1085	c.912_914delCAG	c.(910-915)aacagc>aac	p.S308del	UHRF1BP1_ENST00000452449.2_In_Frame_Del_p.S308del	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	308							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GCAACAGCAACAGCAGCAGCAGC	0.552																																						ENST00000192788.5																			0				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						c.(910-915)aac>aa		UHRF1 binding protein 1																																				SO:0001651	inframe_deletion	54887							g.chr6:34804004_34804006delCAG	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.912_914delCAG	6.37:g.34804013_34804015delCAG	ENSP00000192788:p.Ser308del					UHRF1BP1_ENST00000452449.2_In_Frame_Del_p.NS304del	p.NS304del	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN			8	1083_1085	+			304					Q9NXE0	In_Frame_Del	DEL	ENST00000192788.5	37	c.912_914delCAG	CCDS43455.1																																																																																				0.552	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		7	1299						7	1299	---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34826124	34826124	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:34826124delT	ENST00000192788.5	+	14	2162	c.1991delT	c.(1990-1992)cttfs	p.L664fs	UHRF1BP1_ENST00000452449.2_Frame_Shift_Del_p.L664fs	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	664							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.L666fs*15(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CTGCACATGCTTTTTTTGCAT	0.502																																						ENST00000192788.5																			1	Insertion - Frameshift(1)	p.L666fs*15(1)	breast(1)	breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						c.(1990-1992)ctfs		UHRF1 binding protein 1							170.0	155.0	159.0					6																	34826124		1916	4147	6063	SO:0001589	frameshift_variant	54887							g.chr6:34826124delT	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1991delT	6.37:g.34826124delT	ENSP00000192788:p.Leu664fs					UHRF1BP1_ENST00000452449.2_Frame_Shift_Del_p.L664fs	p.L664fs	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN			14	2162	+			664					Q9NXE0	Frame_Shift_Del	DEL	ENST00000192788.5	37	c.1991delT	CCDS43455.1																																																																																				0.502	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		9	656						9	656	---	---	---	---
C6orf89	221477	broad.mit.edu	37	6	36867371	36867371	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:36867371delC	ENST00000480824.2	+	3	445	c.151delC	c.(151-153)cccfs	p.P53fs	C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000373685.1_Frame_Shift_Del_p.P53fs|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.P60fs			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_ENST00000373685.1_Frame_Shift_Del_p.P53fs|C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.P60fs	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		8	502						8	502	---	---	---	---
FOXP4	116113	broad.mit.edu	37	6	41555186	41555186	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:41555186delC	ENST00000307972.4	+	6	820	c.808delC	c.(808-810)cccfs	p.P271fs	FOXP4_ENST00000373057.3_Frame_Shift_Del_p.P269fs|FOXP4_ENST00000373060.1_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000409208.1_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000373063.3_Frame_Shift_Del_p.P270fs			Q8IVH2	FOXP4_HUMAN	forkhead box P4	271					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CAAGGTCTCACCCCCCCTCTC	0.677											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										ENST00000373060.1																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16						c.(808-810)ccfs		forkhead box P4							67.0	71.0	70.0					6																	41555186		2203	4300	6503	SO:0001589	frameshift_variant	116113				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|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.chr6:41555186delC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.808delC	6.37:g.41555186delC	ENSP00000309823:p.Pro271fs		OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	902	FOXP4_ENST00000409208.1_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000307972.4_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000373057.3_Frame_Shift_Del_p.P269fs|FOXP4_ENST00000373063.3_Frame_Shift_Del_p.P270fs	p.P271fs	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN			7	1266	+	Ovarian(28;0.0327)|Colorectal(47;0.196)		271					Q5W098|Q7Z7F8|Q8IW55|Q96E19	Frame_Shift_Del	DEL	ENST00000307972.4	37	c.808delC	CCDS34447.1																																																																																				0.677	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		7	701						7	701	---	---	---	---
ICK	22858	broad.mit.edu	37	6	52883129	52883129	+	Splice_Site	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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	9	1400						9	1400	---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91296568	91296570	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:91296568_91296570delGAG	ENST00000369329.3	-	1	194_196	c.33_35delCTC	c.(31-36)tcctcg>tcg	p.11_12SS>S	MAP3K7_ENST00000369327.3_In_Frame_Del_p.11_12SS>S|MAP3K7_ENST00000369325.3_In_Frame_Del_p.11_12SS>S|MAP3K7_ENST00000369332.3_In_Frame_Del_p.11_12SS>S	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	11	Interaction with MAPK8IP1. {ECO:0000250}.|Poly-Ser.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		GGCCGAAGACGAGGAGGAGGAGG	0.655																																						ENST00000369329.3																			0				endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28						c.(31-36)tcg>tc		mitogen-activated protein kinase kinase kinase 7																																				SO:0001651	inframe_deletion	6885				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding	g.chr6:91296568_91296570delGAG	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.33_35delCTC	6.37:g.91296577_91296579delGAG	ENSP00000358335:p.Ser14del					MAP3K7_ENST00000369332.3_In_Frame_Del_p.SS13del|MAP3K7_ENST00000369327.3_In_Frame_Del_p.SS13del|MAP3K7_ENST00000369325.3_In_Frame_Del_p.SS13del	p.SS13del	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)	1	194_196	-		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)	13			Poly-Ser.		B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	In_Frame_Del	DEL	ENST00000369329.3	37	c.33_35delCTC	CCDS5028.1																																																																																				0.655	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		7	149						7	149	---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101296336	101296336	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr6:101296336delA	ENST00000369162.2	-	4	833	c.489delT	c.(487-489)tttfs	p.F163fs	ASCC3_ENST00000522650.1_Frame_Shift_Del_p.F163fs	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	163					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AATTTTTACCAAAAAAAACCC	0.333																																						ENST00000369162.2																			0				breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92						c.(487-489)ttfs		activating signal cointegrator 1 complex subunit 3							59.0	54.0	56.0					6																	101296336		2203	4299	6502	SO:0001589	frameshift_variant	10973				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr6:101296336delA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.489delT	6.37:g.101296336delA	ENSP00000358159:p.Phe163fs					ASCC3_ENST00000522650.1_Frame_Shift_Del_p.F163fs	p.F163fs	NM_006828.2	NP_006819.2	Q8N3C0	HELC1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)	4	833	-		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)	163					E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Frame_Shift_Del	DEL	ENST00000369162.2	37	c.489delT	CCDS5046.1																																																																																				0.333	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		7	363						7	363	---	---	---	---
OLIG3	167826	broad.mit.edu	37	6	137815210	137815212	+	In_Frame_Del	DEL	TGG	TGG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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	562						10	562	---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11075380	11075381	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:11075380_11075381delAG	ENST00000403050.3	+	8	2021_2022	c.1569_1570delAG	c.(1567-1572)caagagfs	p.E524fs	PHF14_ENST00000445996.2_Frame_Shift_Del_p.E239fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	524					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		TGTCTTTGCAAGAGAGAGAGAA	0.376																																						ENST00000403050.3																			0				NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35						c.(1567-1572)caagfs		PHD finger protein 14																																				SO:0001589	frameshift_variant	9678						zinc ion binding	g.chr7:11075380_11075381delAG	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1569_1570delAG	7.37:g.11075388_11075389delAG	ENSP00000385795:p.Glu524fs					PHF14_ENST00000445996.2_Frame_Shift_Del_p.QE238fs	p.QE523fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.205)	8	2021_2022	+			523					A7MCZ3|B4DI82	Frame_Shift_Del	DEL	ENST00000403050.3	37	c.1569_1570delAG	CCDS47542.1																																																																																				0.376	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		7	1221						7	1221	---	---	---	---
PPP1R17	10842	broad.mit.edu	37	7	31735179	31735179	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:31735179delA	ENST00000342032.3	+	3	807	c.179delA	c.(178-180)caafs	p.Q60fs	PPP1R17_ENST00000409146.3_Intron	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	60					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)										GAGTCAGACCAAAAAAAACCA	0.438																																						ENST00000342032.3																			0											c.(178-180)cafs		protein phosphatase 1, regulatory subunit 17			,	4,0,4260		0,0,4,0,0,2128	142.0	138.0	140.0		,	3.6	0.8	7		141	1,3,8250		0,0,1,0,3,4123	no	codingComplex,intron	C7orf16	NM_006658.4,NM_001145123.2	,	0,0,5,0,3,6251	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0485,0.0938,0.0639	,	,	31735179	5,3,12510	2203	4300	6503	SO:0001589	frameshift_variant	10842				behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction		g.chr7:31735179delA	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.179delA	7.37:g.31735179delA	ENSP00000340125:p.Gln60fs					PPP1R17_ENST00000409146.3_Intron	p.Q60fs	NM_006658.4	NP_006649.2	O96001	GSUB_HUMAN			3	807	+			60					B4DE58|Q9UDQ0	Frame_Shift_Del	DEL	ENST00000342032.3	37	c.179delA	CCDS5436.1																																																																																				0.438	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658		8	990						8	990	---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39379288	39379290	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:39379288_39379290delCAG	ENST00000403058.1	+	6	713_715	c.559_561delCAG	c.(559-561)cagdel	p.Q196del	POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000518318.2_In_Frame_Del_p.Q196del|POU6F2_ENST00000559001.1_In_Frame_Del_p.Q188del	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	196	Gln-rich.			Q -> QQ (in Ref. 1; AAB49727/AAB49728). {ECO:0000305}.	central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						gctccagctccagcagcagcagc	0.616																																						ENST00000518318.2																			0				NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						c.(559-561)del		POU class 6 homeobox 2																																				SO:0001651	inframe_deletion	11281				central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:39379288_39379290delCAG	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.559_561delCAG	7.37:g.39379297_39379299delCAG	ENSP00000384004:p.Gln196del					POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_In_Frame_Del_p.Q188del|POU6F2_ENST00000403058.1_In_Frame_Del_p.Q196del	p.Q196del			P78424	PO6F2_HUMAN			5	601_603	+			196	Q -> QQ (in Ref. 1; AAB49727/AAB49728).		Gln-rich.		A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	In_Frame_Del	DEL	ENST00000403058.1	37	c.559_561delCAG	CCDS34620.2																																																																																				0.616	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		10	208						10	208	---	---	---	---
INHBA	3624	broad.mit.edu	37	7	41729741	41729743	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:41729741_41729743delTTC	ENST00000242208.4	-	3	1032_1034	c.786_788delGAA	c.(784-789)aagaaa>aaa	p.262_263KK>K	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_In_Frame_Del_p.262_263KK>K|INHBA_ENST00000464515.1_5'UTR	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	262					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ctcctcttctttcttcttcttct	0.581										TSP Lung(11;0.080)																												ENST00000242208.4																			0				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						c.(784-789)aaa>aa		inhibin, beta A																																				SO:0001651	inframe_deletion	3624				cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity	g.chr7:41729741_41729743delTTC		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.786_788delGAA	7.37:g.41729750_41729752delTTC	ENSP00000242208:p.Lys263del	TSP Lung(11;0.080)				INHBA_ENST00000442711.1_In_Frame_Del_p.KK262del|INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA	p.KK262del	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN			3	1032_1034	-			262					Q14599	In_Frame_Del	DEL	ENST00000242208.4	37	c.786_788delGAA	CCDS5464.1																																																																																				0.581	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			8	283						8	283	---	---	---	---
DTX2	113878	broad.mit.edu	37	7	76112249	76112249	+	Frame_Shift_Del	DEL	A	A	-	rs147779783	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:76112249delA	ENST00000324432.5	+	5	1203	c.693delA	c.(691-693)ccafs	p.P231fs	DTX2_ENST00000430490.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000413936.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446600.1_Frame_Shift_Del_p.P140fs|DTX2_ENST00000307569.8_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446820.2_Frame_Shift_Del_p.P231fs	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	231					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						AGCACCCCCCACACAGGACCG	0.657																																						ENST00000324432.5																			0				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						c.(691-693)ccfs		deltex homolog 2 (Drosophila)							125.0	130.0	128.0					7																	76112249		2203	4300	6503	SO:0001589	frameshift_variant	113878				Notch signaling pathway	cytoplasm|nucleus	protein binding|zinc ion binding	g.chr7:76112249delA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.693delA	7.37:g.76112249delA	ENSP00000322885:p.Pro231fs					DTX2_ENST00000413936.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446600.1_Frame_Shift_Del_p.P140fs|DTX2_ENST00000307569.8_Frame_Shift_Del_p.P231fs|DTX2_ENST00000430490.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446820.2_Frame_Shift_Del_p.P231fs	p.P231fs	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN			5	1203	+			231					Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Frame_Shift_Del	DEL	ENST00000324432.5	37	c.693delA	CCDS5587.1																																																																																				0.657	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			8	2045						8	2045	---	---	---	---
TMEM60	85025	broad.mit.edu	37	7	77423460	77423460	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:77423460delT	ENST00000257663.3	-	2	607	c.231delA	c.(229-231)aaafs	p.K77fs		NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	77						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)	4						GGTACCAGGCTTTTTTTTTAA	0.408																																						ENST00000257663.3																			0				endometrium(1)|large_intestine(1)|lung(2)	4						c.(229-231)aafs		transmembrane protein 60							142.0	141.0	141.0					7																	77423460		2203	4300	6503	SO:0001589	frameshift_variant	85025					integral to membrane		g.chr7:77423460delT	AF260336	CCDS5593.1	7q11.23	2005-07-25	2005-07-25	2005-07-25	ENSG00000135211	ENSG00000135211			21754	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 35"""	C7orf35			Standard	NM_032936		Approved	DC32	uc003ugn.3	Q9H2L4	OTTHUMG00000130689	ENST00000257663.3:c.231delA	7.37:g.77423460delT	ENSP00000257663:p.Lys77fs						p.K77fs	NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN			2	607	-			77					A4D1C3|Q86UM0	Frame_Shift_Del	DEL	ENST00000257663.3	37	c.231delA	CCDS5593.1																																																																																				0.408	TMEM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253185.2	NM_032936		20	756						20	756	---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82595385	82595385	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:82595385delT	ENST00000333891.9	-	4	4056	c.3719delA	c.(3718-3720)aagfs	p.K1240fs	PCLO_ENST00000423517.2_Frame_Shift_Del_p.K1240fs	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						AGGGGTTGGCTTTTTTTCTTC	0.383																																						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.(3718-3720)agfs		piccolo presynaptic cytomatrix protein							241.0	235.0	237.0					7																	82595385		1809	4074	5883	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.chr7:82595385delT	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.3719delA	7.37:g.82595385delT	ENSP00000334319:p.Lys1240fs					PCLO_ENST00000333891.8_Frame_Shift_Del_p.K1240fs	p.K1240fs	NM_014510.2	NP_055325.2	Q9Y6V0	PCLO_HUMAN			4	4056	-			1179						Frame_Shift_Del	DEL	ENST00000333891.9	37	c.3719delA	CCDS47630.1																																																																																				0.383	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		8	1917						8	1917	---	---	---	---
SRRT	51593	broad.mit.edu	37	7	100479332	100479332	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:100479332delG	ENST00000347433.4	+	4	462	c.304delG	c.(304-306)gggfs	p.G106fs	SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs|SRRT_ENST00000388793.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	106				G -> GG (in Ref. 3; CAB46374). {ECO:0000305}.	cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.G104fs*45(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GCCCTATGCTGGGGGGGGTGG	0.607																																						ENST00000388793.4																			1	Deletion - Frameshift(1)	p.G104fs*45(1)	ovary(1)	breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						c.(304-306)ggfs		serrate RNA effector molecule homolog (Arabidopsis)			,,,	57,63,4112		1,0,55,5,53,2002	29.0	30.0	30.0		,,,	4.3	1.0	7		30	49,115,8030		0,0,49,12,91,3945	no	codingComplex,codingComplex,codingComplex,codingComplex	SRRT	NM_015908.5,NM_001128854.1,NM_001128853.1,NM_001128852.1	,,,	1,0,104,17,144,5947	A1A1,A1A2,A1R,A2A2,A2R,RR		2.0015,2.8355,2.2855	,,,	,,,	100479332	106,178,12142	2197	4287	6484	SO:0001589	frameshift_variant	51593				cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding	g.chr7:100479332delG		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.304delG	7.37:g.100479332delG	ENSP00000314491:p.Gly106fs					SRRT_ENST00000347433.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs	p.G106fs	NM_001128852.1|NM_015908.5	NP_001122324.1|NP_056992.4	Q9BXP5	SRRT_HUMAN			4	524	+			106	G -> GG (in Ref. 3; CAB46374).				A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	37	c.304delG	CCDS34709.1																																																																																				0.607	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		8	301						8	301	---	---	---	---
WASL	8976	broad.mit.edu	37	7	123332873	123332875	+	In_Frame_Del	DEL	GGA	GGA	-	rs373297831		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:123332873_123332875delGGA	ENST00000223023.4	-	9	1205_1207	c.873_875delTCC	c.(871-876)cctccc>ccc	p.291_292PP>P		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	291	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						gtgtggagggggaggaggaggag	0.567																																						ENST00000223023.4																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(871-876)ccc>cc		Wiskott-Aldrich syndrome-like				46,4176		1,44,2066						-10.8	0.0			50	62,8114		0,62,4026	no	coding	WASL	NM_003941.2		1,106,6092	A1A1,A1R,RR		0.7583,1.0895,0.8711				108,12290				SO:0001651	inframe_deletion	8976				actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity	g.chr7:123332873_123332875delGGA	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.873_875delTCC	7.37:g.123332882_123332884delGGA	ENSP00000223023:p.Pro294del						p.PP293del	NM_003941.2	NP_003932.3	O00401	WASL_HUMAN			9	1205_1207	-			293			Pro-rich.		A1JUI9|Q7Z746	In_Frame_Del	DEL	ENST00000223023.4	37	c.873_875delTCC	CCDS34743.1																																																																																				0.567	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		8	499						8	499	---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135047688	135047688	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr7:135047688delG	ENST00000451834.1	-	12	2365	c.2082delC	c.(2080-2082)cccfs	p.P694fs	CNOT4_ENST00000361528.4_Frame_Shift_Del_p.P623fs|CNOT4_ENST00000473470.1_5'Flank|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.P626fs|CNOT4_ENST00000541284.1_Frame_Shift_Del_p.P697fs			O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	0					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GGGTTTTGCTGGGGGGTCTGA	0.532																																					Ovarian(51;766 1130 5502 35047 50875)	ENST00000541284.1																			0				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						c.(2089-2091)ccfs		CCR4-NOT transcription complex, subunit 4							187.0	196.0	193.0					7																	135047688		1847	4095	5942	SO:0001589	frameshift_variant	4850				nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr7:135047688delG	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000451834.1:c.2082delC	7.37:g.135047688delG	ENSP00000388491:p.Pro694fs					CNOT4_ENST00000451834.1_Frame_Shift_Del_p.P694fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.P623fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.P626fs	p.P697fs	NM_001190849.1|NM_001190850.1	NP_001177778.1|NP_001177779.1	O95628	CNOT4_HUMAN			12	2421	-			366					B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Frame_Shift_Del	DEL	ENST00000451834.1	37	c.2091delC	CCDS55167.1																																																																																				0.532	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316		7	2164						7	2164	---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6289099	6289099	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:6289099delA	ENST00000344683.5	+	4	389	c.313delA	c.(313-315)aaafs	p.K107fs	MCPH1_ENST00000522905.1_Frame_Shift_Del_p.K107fs|MCPH1_ENST00000519480.1_Frame_Shift_Del_p.K107fs	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	107					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AAGCCTAATTAAAAAAAAAGT	0.274																																					Colon(95;1448 1467 8277 34473 35819)	ENST00000344683.5																		AGPAT5/MCPH1(2)	0				central_nervous_system(1)|large_intestine(4)|skin(1)	6						c.(313-315)aafs		microcephalin 1							83.0	81.0	82.0					8																	6289099		1811	4070	5881	SO:0001589	frameshift_variant	79648					microtubule organizing center		g.chr8:6289099delA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.313delA	8.37:g.6289099delA	ENSP00000342924:p.Lys107fs					MCPH1_ENST00000522905.1_Frame_Shift_Del_p.K107fs|MCPH1_ENST00000519480.1_Frame_Shift_Del_p.K107fs	p.K107fs	NM_024596.3	NP_078872.2	Q8NEM0	MCPH1_HUMAN		Colorectal(4;0.0505)	4	389	+		Hepatocellular(245;0.0663)	107					B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Frame_Shift_Del	DEL	ENST00000344683.5	37	c.313delA	CCDS43689.1																																																																																				0.274	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		10	484						10	484	---	---	---	---
FAM66B	100128890	broad.mit.edu	37	8	7196263	7196264	+	lincRNA	DEL	AC	AC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:7196263_7196264delAC	ENST00000606573.1	-	0	703									family with sequence similarity 66, member B																		ACTGAGGGGTacacacacacac	0.5																																						ENST00000606573.1																			0																																																			0							g.chr8:7196263_7196264delAC			8p23.1	2013-07-05			ENSG00000215374	ENSG00000215374		"""Long non-coding RNAs"""	28890	non-coding RNA	RNA, long non-coding							Standard	NR_027423		Approved				OTTHUMG00000165383		8.37:g.7196273_7196274delAC														0	703	-									RNA	DEL	ENST00000606573.1	37																																																																																						0.500	FAM66B-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470344.1	NR_027423		8	15						8	15	---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12958019	12958019	+	Frame_Shift_Del	DEL	G	G	-	rs145646504		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:12958019delG	ENST00000276297.4	-	9	2236	c.1827delC	c.(1825-1827)cccfs	p.P609fs	DLC1_ENST00000358919.2_Frame_Shift_Del_p.P172fs|DLC1_ENST00000520226.1_Frame_Shift_Del_p.P98fs|DLC1_ENST00000512044.2_Frame_Shift_Del_p.P206fs	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	609					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CATCCTCGCTGGGGGGCGCGT	0.672																																						ENST00000276297.4																			0				NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						c.(1825-1827)ccfs		deleted in liver cancer 1							38.0	45.0	42.0					8																	12958019		2200	4298	6498	SO:0001589	frameshift_variant	10395				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding	g.chr8:12958019delG	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1827delC	8.37:g.12958019delG	ENSP00000276297:p.Pro609fs					DLC1_ENST00000512044.2_Frame_Shift_Del_p.P206fs|DLC1_ENST00000520226.1_Frame_Shift_Del_p.P98fs|DLC1_ENST00000358919.2_Frame_Shift_Del_p.P172fs	p.P609fs	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN			9	2236	-			609					B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Frame_Shift_Del	DEL	ENST00000276297.4	37	c.1827delC	CCDS5989.1																																																																																				0.672	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		7	662						7	662	---	---	---	---
NUGGC	389643	broad.mit.edu	37	8	27888776	27888776	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:27888776delT	ENST00000413272.2	-	15	2034	c.1892delA	c.(1891-1893)aatfs	p.N631fs	NUGGC_ENST00000341513.6_Frame_Shift_Del_p.N631fs	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	631					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										GATCAGGAAATTTTTTTTGCA	0.453																																						ENST00000413272.2																			0											c.(1891-1893)atfs		nuclear GTPase, germinal center associated							167.0	171.0	170.0					8																	27888776		1899	4103	6002	SO:0001589	frameshift_variant	389643							g.chr8:27888776delT	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1892delA	8.37:g.27888776delT	ENSP00000408697:p.Asn631fs					NUGGC_ENST00000341513.6_Frame_Shift_Del_p.N631fs	p.N631fs	NM_001010906.1	NP_001010906.1					15	2034	-								Q6ZP73	Frame_Shift_Del	DEL	ENST00000413272.2	37	c.1892delA	CCDS47833.1																																																																																				0.453	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		9	1163						9	1163	---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30695491	30695491	+	Frame_Shift_Del	DEL	T	T	-	rs571456178		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:30695491delT	ENST00000256246.2	-	3	7234	c.7160delA	c.(7159-7161)aagfs	p.K2387fs		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2387					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CATTTCAACCTTTTTTGGCGT	0.388																																						ENST00000256246.2																			0				NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138						c.(7159-7161)agfs		testis expressed 15							183.0	183.0	183.0					8																	30695491		2203	4300	6503	SO:0001589	frameshift_variant	56154							g.chr8:30695491delT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.7160delA	8.37:g.30695491delT	ENSP00000256246:p.Lys2387fs						p.K2387fs	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	3	7234	-			2387						Frame_Shift_Del	DEL	ENST00000256246.2	37	c.7160delA	CCDS6080.1																																																																																				0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			7	910						7	910	---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38285914	38285916	+	In_Frame_Del	DEL	TCA	TCA	-	rs138489552		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:38285914_38285916delTCA	ENST00000447712.2	-	4	1337_1339	c.396_398delTGA	c.(394-399)gatgac>gac	p.132_133DD>D	FGFR1_ENST00000397113.2_In_Frame_Del_p.132_133DD>D|FGFR1_ENST00000326324.6_In_Frame_Del_p.43_44DD>D|FGFR1_ENST00000397108.4_In_Frame_Del_p.132_133DD>D|FGFR1_ENST00000425967.3_In_Frame_Del_p.165_166DD>D|FGFR1_ENST00000335922.5_In_Frame_Del_p.124_125DD>D|FGFR1_ENST00000397091.5_In_Frame_Del_p.132_133DD>D|FGFR1_ENST00000532791.1_In_Frame_Del_p.132_133DD>D|FGFR1_ENST00000341462.5_In_Frame_Del_p.135_136DD>D|RP11-350N15.4_ENST00000528407.1_RNA|FGFR1_ENST00000397103.1_In_Frame_Del_p.43_44DD>D|FGFR1_ENST00000356207.5_In_Frame_Del_p.43_44DD>D	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	132					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.D133N(3)|p.D44N(1)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	TGAAGAGGAGtcatcatcatcat	0.498		1	T	"""BCR, FOP, ZNF198, CEP1"""	"""MPD, NHL"""		"""Pfeiffer syndrome, Kallman syndrome"""																														Melanoma(146;1153 1840 21453 21841 43625)	ENST00000447712.2		1		Dom	yes		8	8p11.2-p11.1	2260	T	fibroblast growth factor receptor 1	yes	"""Pfeiffer syndrome, Kallman syndrome"""	L	"""BCR, FOP, ZNF198, CEP1"""		"""MPD, NHL"""	FGFR1/ZNF703(2)	4	Substitution - Missense(4)	p.D133N(3)|p.D44N(1)	stomach(4)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50						c.(394-399)gac>ga		fibroblast growth factor receptor 1	Palifermin(DB00039)		,,,,,,,,	46,3694		0,46,1824					,,,,,,,,	3.9	1.0		dbSNP_134	170	127,7795		0,127,3834	no	coding,coding,coding,coding,coding,coding,coding,coding,coding	FGFR1	NM_023110.2,NM_023106.2,NM_023105.2,NM_015850.3,NM_001174067.1,NM_001174066.1,NM_001174065.1,NM_001174064.1,NM_001174063.1	,,,,,,,,	0,173,5658	A1A1,A1R,RR		1.6031,1.2299,1.4835	,,,,,,,,	,,,,,,,,		173,11489				SO:0001651	inframe_deletion	2260				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity	g.chr8:38285914_38285916delTCA	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3688	protein-coding gene	gene with protein product	"""Pfeiffer syndrome"""	136350	"""fms-related tyrosine kinase 2"""	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.396_398delTGA	8.37:g.38285923_38285925delTCA	ENSP00000400162:p.Asp133del					FGFR1_ENST00000532791.1_In_Frame_Del_p.DD132del|FGFR1_ENST00000341462.5_In_Frame_Del_p.DD135del|FGFR1_ENST00000425967.3_In_Frame_Del_p.DD165del|FGFR1_ENST00000397091.5_In_Frame_Del_p.DD132del|FGFR1_ENST00000397103.1_In_Frame_Del_p.DD43del|FGFR1_ENST00000335922.5_In_Frame_Del_p.DD124del|FGFR1_ENST00000397108.4_In_Frame_Del_p.DD132del|FGFR1_ENST00000397113.2_In_Frame_Del_p.DD132del|FGFR1_ENST00000356207.5_In_Frame_Del_p.DD43del|FGFR1_ENST00000326324.6_In_Frame_Del_p.DD43del	p.DD132del	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		4	1337_1339	-	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	132					A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	In_Frame_Del	DEL	ENST00000447712.2	37	c.396_398delTGA	CCDS6107.2																																																																																				0.498	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				13	277						13	277	---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48746799	48746799	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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_ENST00000338368.3_Frame_Shift_Del_p.R2703fs|PRKDC_ENST00000523565.1_5'UTR	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		10	2001						10	2001	---	---	---	---
TERF1	7013	broad.mit.edu	37	8	73921284	73921286	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:73921284_73921286delGAG	ENST00000276603.5	+	1	186_188	c.163_165delGAG	c.(163-165)gagdel	p.E62del	TERF1_ENST00000276602.6_In_Frame_Del_p.E62del	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	62	Asp/Glu-rich (acidic).|Poly-Glu.|TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			GGGGGCCCCCgaggaggaggagg	0.65																																						ENST00000276602.6																			0				central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9						c.(163-165)del		telomeric repeat binding factor (NIMA-interacting) 1																																				SO:0001651	inframe_deletion	7013				age-dependent telomere shortening|cell division|G2/M transition of mitotic cell cycle|induction of apoptosis|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of telomere maintenance via semi-conservative replication|negative regulation of telomere maintenance via telomerase|positive regulation of microtubule polymerization|positive regulation of mitosis|positive regulation of mitotic cell cycle|protein homooligomerization|regulation of transcription, DNA-dependent|telomere maintenance via telomerase|telomere maintenance via telomere shortening	chromosome, telomeric region|cytoplasm|nuclear telomere cap complex|nucleoplasm|nucleus|spindle	caspase activator activity|DNA bending activity|double-stranded telomeric DNA binding|identical protein binding|microtubule binding|protein heterodimerization activity|protein homodimerization activity|telomerase inhibitor activity|telomeric DNA binding	g.chr8:73921284_73921286delGAG	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.163_165delGAG	8.37:g.73921293_73921295delGAG	ENSP00000276603:p.Glu62del					TERF1_ENST00000276603.5_In_Frame_Del_p.E62del	p.E62del	NM_003218.3	NP_003209.2	P54274	TERF1_HUMAN	Epithelial(68;0.0984)		1	186_188	+	Breast(64;0.218)		62			Asp/Glu-rich (acidic).|Poly-Glu.|TRFH dimerization.		A7XP29|Q15553|Q8NHT6|Q93029	In_Frame_Del	DEL	ENST00000276603.5	37	c.163_165delGAG	CCDS6211.1																																																																																				0.650	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		11	175						11	175	---	---	---	---
TP53INP1	94241	broad.mit.edu	37	8	95952409	95952411	+	In_Frame_Del	DEL	TCT	TCT	-	rs548441545|rs563445319	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:95952409_95952411delTCT	ENST00000342697.4	-	3	557_559	c.150_152delAGA	c.(148-153)gaagag>gag	p.50_51EE>E	TP53INP1_ENST00000378776.4_In_Frame_Del_p.50_51EE>E|NDUFAF6_ENST00000396113.1_Intron|TP53INP1_ENST00000448464.2_In_Frame_Del_p.50_51EE>E	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	50	Glu-rich.				apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to hydroperoxide (GO:0071447)|cellular response to methyl methanesulfonate (GO:0072703)|cellular response to UV (GO:0034644)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|response to heat (GO:0009408)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)	p.E50E(1)		kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9	Breast(36;8.75e-07)					GATGTCCTCCTCTTCTTCTTCTT	0.458														16	0.00319489	0.0045	0.0014	5008	,	,		22458	0.0		0.001	False		,,,				2504	0.0082					ENST00000342697.4																			1	Substitution - coding silent(1)	p.E50E(1)	large_intestine(1)	kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9						c.(148-153)gag>ga		tumor protein p53 inducible nuclear protein 1			,	50,2,4210		0,0,50,0,2,2079					,	-3.8	0.0			119	68,3,8183		0,0,68,0,3,4056	no	codingComplex,codingComplex	TP53INP1	NM_033285.3,NM_001135733.1	,	0,0,118,0,5,6135	A1A1,A1A2,A1R,A2A2,A2R,RR		0.8602,1.2201,0.9827	,	,		118,5,12393				SO:0001651	inframe_deletion	0				apoptosis	PML body		g.chr8:95952409_95952411delTCT	AF409115	CCDS6265.1, CCDS47899.1	8q22	2004-03-11				ENSG00000164938			18022	protein-coding gene	gene with protein product		606185				11511362, 12438758	Standard	NM_033285		Approved	DKFZp434M1317, FLJ22139, P53DINP1, SIP, TP53INP1A, TP53INP1B, Teap	uc003yhg.3	Q96A56		ENST00000342697.4:c.150_152delAGA	8.37:g.95952418_95952420delTCT	ENSP00000344215:p.Glu52del					TP53INP1_ENST00000378776.4_In_Frame_Del_p.EE50del|TP53INP1_ENST00000448464.2_In_Frame_Del_p.EE50del|NDUFAF6_ENST00000396113.1_Intron	p.EE50del	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN			3	557_559	-	Breast(36;8.75e-07)		50			Glu-rich.		B2RCE5|Q969R9	In_Frame_Del	DEL	ENST00000342697.4	37	c.150_152delAGA	CCDS6265.1																																																																																				0.458	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1			9	297						9	297	---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105440214	105440214	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:105440214delT	ENST00000351513.2	-	6	1218	c.1086delA	c.(1084-1086)aaafs	p.K362fs	AP003471.2_ENST00000410226.1_RNA	NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	362					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCACCACGCCTTTTTCCCATA	0.478																																						ENST00000351513.2																			0				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(1084-1086)aafs		dihydropyrimidinase							179.0	176.0	177.0					8																	105440214		2203	4300	6503	SO:0001589	frameshift_variant	1807				protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding	g.chr8:105440214delT	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.1086delA	8.37:g.105440214delT	ENSP00000276651:p.Lys362fs						p.K362fs	NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)		6	1218	-			362						Frame_Shift_Del	DEL	ENST00000351513.2	37	c.1086delA	CCDS6302.1																																																																																				0.478	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		19	1644						19	1644	---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110455173	110455174	+	Splice_Site	INS	-	-	G	rs375659563		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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	11	529						11	529	---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124384893	124384893	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:124384893delT	ENST00000287394.5	-	3	461	c.354delA	c.(352-354)aaafs	p.K118fs	ATAD2_ENST00000521903.1_5'UTR	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	118					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E119fs*8(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TGTGCTCTTCTTTTTTTTTAT	0.269																																						ENST00000287394.5																			1	Deletion - Frameshift(1)	p.E119fs*8(1)	large_intestine(1)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48						c.(352-354)aafs		ATPase family, AAA domain containing 2							144.0	150.0	148.0					8																	124384893		2201	4297	6498	SO:0001589	frameshift_variant	29028				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity	g.chr8:124384893delT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.354delA	8.37:g.124384893delT	ENSP00000287394:p.Lys118fs					ATAD2_ENST00000521903.1_5'UTR	p.K118fs	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	STAD - Stomach adenocarcinoma(47;0.00288)		3	461	-	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		118					Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Frame_Shift_Del	DEL	ENST00000287394.5	37	c.354delA	CCDS6343.1																																																																																				0.269	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		9	878						9	878	---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145000951	145000953	+	Splice_Site	DEL	CCT	CCT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:145000951_145000953delCCT	ENST00000322810.4	-	30	4623_4625	c.4454_4456delAGG	c.(4453-4458)gagggg>ggg	p.E1485del	PLEC_ENST00000354958.2_Splice_Site_p.E1326del|PLEC_ENST00000436759.2_Splice_Site_p.E1375del|PLEC_ENST00000527096.1_Splice_Site_p.E1371del|PLEC_ENST00000345136.3_Splice_Site_p.E1348del|PLEC_ENST00000398774.2_Splice_Site_p.E1316del|PLEC_ENST00000357649.2_Splice_Site_p.E1352del|PLEC_ENST00000356346.3_Splice_Site_p.E1334del|PLEC_ENST00000354589.3_Splice_Site_p.E1348del	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1485	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						ACGGGCTGTACCTCCTCCTCCTC	0.621																																						ENST00000322810.4																			0				NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						c.e30+1		plectin																																				SO:0001630	splice_region_variant	5339				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle	g.chr8:145000951_145000953delCCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4455+1AGG>-	8.37:g.145000960_145000962delCCT						PLEC_ENST00000354958.2_Splice_Site_p.G1326_splice|PLEC_ENST00000356346.3_Splice_Site_p.G1334_splice|PLEC_ENST00000354589.3_Splice_Site_p.G1348_splice|PLEC_ENST00000527096.1_Splice_Site_p.G1371_splice|PLEC_ENST00000436759.2_Splice_Site_p.G1375_splice|PLEC_ENST00000357649.2_Splice_Site_p.G1352_splice|PLEC_ENST00000398774.2_Splice_Site_p.G1316_splice|PLEC_ENST00000345136.3_Splice_Site_p.G1348_splice	p.G1485_splice	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN			30	4623_4625	-			1485			Central fibrous rod domain.		Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Splice_Site	DEL	ENST00000322810.4	37	c.4455_splice	CCDS43772.1																																																																																				0.621	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	In_Frame_Del	7	763						7	763	---	---	---	---
KIFC2	90990	broad.mit.edu	37	8	145692926	145692926	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr8:145692926delG	ENST00000301332.2	+	5	905	c.528delG	c.(526-528)ctgfs	p.L176fs	CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000438911.2_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|KIFC2_ENST00000301331.5_5'Flank|CYHR1_ENST00000306145.5_5'Flank|CYHR1_ENST00000403000.2_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	176					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GCGAGCCACTGGGGGATGAGA	0.627											OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000301332.2																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19						c.(526-528)ctfs		kinesin family member C2							63.0	67.0	66.0					8																	145692926		2202	4300	6502	SO:0001589	frameshift_variant	90990				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding	g.chr8:145692926delG	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"""Kinesins"""	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.528delG	8.37:g.145692926delG	ENSP00000301332:p.Leu176fs		OREG0019057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1696		p.L176fs	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)		5	905	+	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		176					E9PHB2|Q96NN6	Frame_Shift_Del	DEL	ENST00000301332.2	37	c.528delG	CCDS6427.1																																																																																				0.627	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		7	852						7	852	---	---	---	---
NOL6	65083	broad.mit.edu	37	9	33466944	33466944	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:33466944delC	ENST00000379471.2	-	15	2003	c.1916delG	c.(1915-1917)ggcfs	p.G639fs	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Frame_Shift_Del_p.G587fs			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	639					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		ATCCAGGGGGCCCCCCACATA	0.517											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000379471.2																			0				endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27						c.(1915-1917)gcfs		nucleolar protein 6 (RNA-associated)							199.0	218.0	212.0					9																	33466944		2203	4300	6503	SO:0001589	frameshift_variant	65083				rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding	g.chr9:33466944delC	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1916delG	9.37:g.33466944delC	ENSP00000368784:p.Gly639fs		OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	840	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Frame_Shift_Del_p.G587fs	p.G639fs			Q9H6R4	NOL6_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)	15	2003	-			639					Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Frame_Shift_Del	DEL	ENST00000379471.2	37	c.1916delG																																																																																					0.517	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		9	2257						9	2257	---	---	---	---
VCP	7415	broad.mit.edu	37	9	35062983	35062985	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:35062983_35062985delAAG	ENST00000358901.6	-	7	1696_1698	c.801_803delCTT	c.(799-804)ttcttg>ttg	p.F267del		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	267					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ACCATTGATCAAGAAGAAGAAGG	0.463																																						ENST00000358901.6																			0				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						c.(799-804)ttg>tt		valosin containing protein																																				SO:0001651	inframe_deletion	7415				activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding	g.chr9:35062983_35062985delAAG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.801_803delCTT	9.37:g.35062992_35062994delAAG	ENSP00000351777:p.Phe267del						p.FL267del	NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)		7	1696_1698	-			267					B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	In_Frame_Del	DEL	ENST00000358901.6	37	c.801_803delCTT	CCDS6573.1																																																																																				0.463	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		7	1010						7	1010	---	---	---	---
KGFLP2	654466	broad.mit.edu	37	9	41962602	41962602	+	lincRNA	DEL	G	G	-	rs201713470	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:41962602delG	ENST00000454645.1	-	0	902					NR_003670.1																						TTCTTTCTTTGTTTTTTTTCC	0.373																																						ENST00000454645.1																			0																																																			0							g.chr9:41962602delG																													9.37:g.41962602delG								NR_003670.1						0	902	-									RNA	DEL	ENST00000454645.1	37																																																																																						0.373	RP11-204M4.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000143738.1			13	321						13	321	---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95277132	95277134	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:95277132_95277134delCCT	ENST00000344604.5	-	4	982_984	c.833_835delAGG	c.(832-837)gagggt>ggt	p.E278del	ECM2_ENST00000444490.2_In_Frame_Del_p.E256del|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	278	Poly-Glu.				cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ccctcctcaccctcctcctcctc	0.611																																						ENST00000344604.5																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						c.(832-837)ggt>g		extracellular matrix protein 2, female organ and adipocyte specific																																				SO:0001651	inframe_deletion	1842				cell-matrix adhesion		integrin binding	g.chr9:95277132_95277134delCCT	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.833_835delAGG	9.37:g.95277141_95277143delCCT	ENSP00000344758:p.Glu278del					CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_In_Frame_Del_p.EG256del	p.EG278del	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN			4	982_984	-			278			Poly-Glu.		B2R730|E2PU11|Q5T9F2|Q7Z3D0	In_Frame_Del	DEL	ENST00000344604.5	37	c.833_835delAGG	CCDS6698.1																																																																																				0.611	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		7	758						7	758	---	---	---	---
HABP4	22927	broad.mit.edu	37	9	99250415	99250416	+	Frame_Shift_Ins	INS	-	-	C	rs372277294		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:99250415_99250416insC	ENST00000375249.4	+	7	1119_1120	c.1044_1045insC	c.(1045-1047)cccfs	p.P349fs	HABP4_ENST00000466976.1_3'UTR|HABP4_ENST00000375251.3_Frame_Shift_Ins_p.P244fs	NM_014282.2	NP_055097.2			hyaluronan binding protein 4											NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				TTTTCCGGAAACCCGCCAATGA	0.53																																						ENST00000375249.4																			0				NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						c.(1042-1047)aaccgcfs		hyaluronan binding protein 4																																				SO:0001589	frameshift_variant	22927				platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding	g.chr9:99250415_99250416insC	AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.1047dupC	9.37:g.99250418_99250418dupC	ENSP00000364398:p.Pro349fs					HABP4_ENST00000466976.1_3'UTR|HABP4_ENST00000375251.3_Frame_Shift_Ins_p.R244fs	p.R349fs	NM_014282.2	NP_055097.2	Q5JVS0	HABP4_HUMAN			7	1119_1120	+		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)	349						Frame_Shift_Ins	INS	ENST00000375249.4	37	c.1044_1045insC	CCDS6719.1																																																																																				0.530	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	NM_014282		15	767						15	767	---	---	---	---
WDR5	11091	broad.mit.edu	37	9	137019598	137019598	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr9:137019598delC	ENST00000358625.3	+	10	813	c.642delC	c.(640-642)aacfs	p.N214fs	WDR5_ENST00000425041.1_Frame_Shift_Del_p.N214fs	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	214					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		ATGACGACAACCCCCCCGTGT	0.627																																						ENST00000358625.3																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9						c.(640-642)aafs		WD repeat domain 5							250.0	223.0	232.0					9																	137019598		2203	4300	6503	SO:0001589	frameshift_variant	11091				histone H3 acetylation|histone H3-K4 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ada2/Gcn5/Ada3 transcription activator complex|MLL1 complex|Set1C/COMPASS complex	protein binding	g.chr9:137019598delC	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.642delC	9.37:g.137019598delC	ENSP00000351446:p.Asn214fs					WDR5_ENST00000425041.1_Frame_Shift_Del_p.N214fs	p.N214fs	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)	10	813	+		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)	214					Q91VA5|Q9NWX7|Q9UGP9	Frame_Shift_Del	DEL	ENST00000358625.3	37	c.642delC	CCDS6981.1																																																																																				0.627	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821		10	2139						10	2139	---	---	---	---
ANK3	288	broad.mit.edu	37	10	61828745	61828747	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:61828745_61828747delGTG	ENST00000280772.2	-	37	12083_12085	c.11892_11894delCAC	c.(11890-11895)accact>act	p.3964_3965TT>T	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3964	Thr-rich.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						ggtggtggcagtggtggtggtgg	0.498																																						ENST00000280772.1																			0				NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						c.(11890-11895)act>ac		ankyrin 3, node of Ranvier (ankyrin G)																																				SO:0001651	inframe_deletion	288				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding	g.chr10:61828745_61828747delGTG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11892_11894delCAC	10.37:g.61828754_61828756delGTG	ENSP00000280772:p.Thr3965del					ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	p.TT3964del	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN			37	12083_12085	-			3964			Thr-rich.		B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	In_Frame_Del	DEL	ENST00000280772.2	37	c.11892_11894delCAC	CCDS7258.1																																																																																				0.498	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		7	769						7	769	---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70156583	70156583	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:70156583delT	ENST00000602465.1	-	4	452	c.352delA	c.(352-354)atgfs	p.M118fs	RUFY2_ENST00000454950.2_Frame_Shift_Del_p.M60fs|RUFY2_ENST00000388768.2_Frame_Shift_Del_p.M153fs|RUFY2_ENST00000399200.2_Intron|RUFY2_ENST00000342616.4_Frame_Shift_Del_p.M118fs|RUFY2_ENST00000472394.2_5'UTR			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	167	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						TAATCGGCCATTTTTTTTTGC	0.398																																						ENST00000388768.2																			0				NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						c.(457-459)tgfs		RUN and FYVE domain containing 2							81.0	80.0	81.0					10																	70156583		1832	4087	5919	SO:0001589	frameshift_variant	55680					nucleus	metal ion binding	g.chr10:70156583delT	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"""Zinc fingers, FYVE domain containing"""	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.352delA	10.37:g.70156583delT	ENSP00000473462:p.Met118fs					RUFY2_ENST00000602465.1_Frame_Shift_Del_p.M118fs|RUFY2_ENST00000342616.4_Frame_Shift_Del_p.M118fs|RUFY2_ENST00000454950.2_Frame_Shift_Del_p.M60fs|RUFY2_ENST00000399200.2_Intron|RUFY2_ENST00000472394.2_5'UTR	p.M153fs	NM_017987.4	NP_060457.4	Q8WXA3	RUFY2_HUMAN			4	783	-			167			RUN.		B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Frame_Shift_Del	DEL	ENST00000602465.1	37	c.457delA																																																																																					0.398	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		21	358						21	358	---	---	---	---
PSD	5662	broad.mit.edu	37	10	104176574	104176574	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:104176574delG	ENST00000020673.5	-	2	748	c.222delC	c.(220-222)cccfs	p.P74fs	PSD_ENST00000406432.1_Frame_Shift_Del_p.P74fs|FBXL15_ENST00000224862.3_5'Flank|PSD_ENST00000492902.2_5'UTR	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	74	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)	p.S75fs*127(1)		breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CACGGGGTGAGGGGGGGCCAC	0.672																																						ENST00000020673.5																			1	Insertion - Frameshift(1)	p.S75fs*127(1)	ovary(1)	breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						c.(220-222)ccfs		pleckstrin and Sec7 domain containing							38.0	43.0	42.0					10																	104176574		2192	4282	6474	SO:0001589	frameshift_variant	5662				regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity	g.chr10:104176574delG	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.222delC	10.37:g.104176574delG	ENSP00000020673:p.Pro74fs					PSD_ENST00000406432.1_Frame_Shift_Del_p.P74fs|PSD_ENST00000492902.2_5'UTR	p.P74fs	NM_001270966.1|NM_002779.3	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN		Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)	2	748	-			74			Pro-rich.		B1AKX7|D3DR87|Q15673|Q8IVG0	Frame_Shift_Del	DEL	ENST00000020673.5	37	c.222delC	CCDS31272.1																																																																																				0.672	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			8	633						8	633	---	---	---	---
SLK	9748	broad.mit.edu	37	10	105727547	105727549	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:105727547_105727549delAGA	ENST00000369755.3	+	1	589_591	c.44_46delAGA	c.(43-48)gagaag>gag	p.K19del	SLK_ENST00000335753.4_In_Frame_Del_p.K19del	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	19	Poly-Lys.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TTGGGGAGCGAGAAGAAGAAGAA	0.448																																					NSCLC(111;540 1651 1927 4474 17706)	ENST00000369755.3																			0				kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8						c.(43-48)gag>g		STE20-like kinase																																				SO:0001651	inframe_deletion	9748				apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity	g.chr10:105727547_105727549delAGA		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.44_46delAGA	10.37:g.105727556_105727558delAGA	ENSP00000358770:p.Lys19del					SLK_ENST00000335753.4_In_Frame_Del_p.EK15del	p.EK15del	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)	1	589_591	+		Colorectal(252;0.178)	15					D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	In_Frame_Del	DEL	ENST00000369755.3	37	c.44_46delAGA	CCDS7553.1																																																																																				0.448	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		9	711						9	711	---	---	---	---
IKZF5	64376	broad.mit.edu	37	10	124758126	124758127	+	Frame_Shift_Ins	INS	-	-	T	rs202154688		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:124758126_124758127insT	ENST00000368886.5	-	3	335_336	c.15_16insA	c.(13-18)aaaccafs	p.P6fs	IKZF5_ENST00000479103.1_5'UTR	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	6					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		AAAGGCTCTGGTTTTTTTTCAC	0.371																																						ENST00000368886.5																			0				endometrium(2)|lung(3)|prostate(1)	6						c.(13-18)aacagafs		IKAROS family zinc finger 5 (Pegasus)																																				SO:0001589	frameshift_variant	64376				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr10:124758126_124758127insT	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	14283	protein-coding gene	gene with protein product		606238	"""zinc finger protein, subfamily 1A, 5"", ""zinc finger protein, subfamily 1A, 5 (Pegasus)"""	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.16dupA	10.37:g.124758134_124758134dupT	ENSP00000357881:p.Pro6fs					IKZF5_ENST00000479103.1_5'UTR	p.NR5fs	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)	3	335_336	-		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)	5					B3KVH7|D3DRE7|Q9H2T0	Frame_Shift_Ins	INS	ENST00000368886.5	37	c.15_16insA	CCDS41574.1																																																																																				0.371	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466		7	496						7	496	---	---	---	---
CPXM2	119587	broad.mit.edu	37	10	125528165	125528167	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:125528165_125528167delCAG	ENST00000241305.3	-	9	1328_1330	c.1174_1176delCTG	c.(1174-1176)ctgdel	p.L392del	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	392	Poly-Leu.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		CGAACTGCACCAGCAGCAGCAGC	0.626																																						ENST00000241305.3																			0				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47						c.(1174-1176)del		carboxypeptidase X (M14 family), member 2																																				SO:0001651	inframe_deletion	119587				cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding	g.chr10:125528165_125528167delCAG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1174_1176delCTG	10.37:g.125528174_125528176delCAG	ENSP00000241305:p.Leu392del					CPXM2_ENST00000368854.3_5'UTR	p.L392del	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)	9	1328_1330	-		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)	392			Poly-Leu.		B4E3Q2	In_Frame_Del	DEL	ENST00000241305.3	37	c.1174_1176delCTG	CCDS7637.1																																																																																				0.626	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		9	950						9	950	---	---	---	---
FRG2B	441581	broad.mit.edu	37	10	135438960	135438960	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr10:135438960delC	ENST00000425520.1	-	4	532	c.480delG	c.(478-480)aggfs	p.R160fs	FRG2B_ENST00000443774.1_Frame_Shift_Del_p.R161fs	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	160						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGGCCCGAGACCTATGCCGCT	0.557																																						ENST00000443774.1																			0				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20						c.(481-483)agfs		FSHD region gene 2 family, member B							117.0	141.0	133.0					10																	135438960		2195	4299	6494	SO:0001589	frameshift_variant	441581					nucleus		g.chr10:135438960delC	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.480delG	10.37:g.135438960delC	ENSP00000401310:p.Arg160fs					FRG2B_ENST00000425520.1_Frame_Shift_Del_p.R160fs	p.R161fs			Q96QU4	FRG2B_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	4	532	-		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)	160					Q5VSQ1	Frame_Shift_Del	DEL	ENST00000425520.1	37	c.483delG	CCDS44502.1																																																																																				0.557	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998		18	883						18	883	---	---	---	---
KRTAP5-5	439915	broad.mit.edu	37	11	1651191	1651199	+	In_Frame_Del	DEL	GGCTGTGGA	GGCTGTGGA	-	rs71025763|rs144216147	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:1651191_1651199delGGCTGTGGA	ENST00000399676.2	+	1	159_167	c.121_129delGGCTGTGGA	c.(121-129)ggctgtggadel	p.GCG47del		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ctgtggctccggctgtggaggctgtgggg	0.713																																						ENST00000399676.2																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33						c.(121-129)del		keratin associated protein 5-5				727,2515		74,579,968						1.8	0.6		dbSNP_130	24	1587,5219		143,1301,1959	no	coding	KRTAP5-5	NM_001001480.2		217,1880,2927	A1A1,A1R,RR		23.3177,22.4244,23.0295				2314,7734				SO:0001651	inframe_deletion	439915					keratin filament		g.chr11:1651191_1651199delGGCTGTGGA	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.121_129delGGCTGTGGA	11.37:g.1651191_1651199delGGCTGTGGA	ENSP00000382584:p.Gly47_Gly49del						p.GCG47del	NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	1	159_167	+		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	47					A8MWN2	In_Frame_Del	DEL	ENST00000399676.2	37	c.121_129delGGCTGTGGA	CCDS41592.1																																																																																				0.713	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			7	599						7	599	---	---	---	---
TSSC4	10078	broad.mit.edu	37	11	2424492	2424493	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:2424492_2424493insG	ENST00000333256.6	+	3	1072_1073	c.629_630insG	c.(628-633)gaggggfs	p.EG210fs	TSSC4_ENST00000467308.1_Intron|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000451491.2_Frame_Shift_Ins_p.EG210fs|TSSC4_ENST00000380996.5_Frame_Shift_Ins_p.EG146fs			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	210										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGCTGTGGGGAGGGGAGGGTCA	0.658																																						ENST00000333256.6																			0				endometrium(3)|large_intestine(1)|lung(4)	8						c.(628-630)gggfs		tumor suppressing subtransferable candidate 4																																				SO:0001589	frameshift_variant	10078							g.chr11:2424492_2424493insG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.633dupG	11.37:g.2424496_2424496dupG	ENSP00000331087:p.Glu210fs					TSSC4_ENST00000380996.5_Frame_Shift_Ins_p.G146fs|TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000467308.1_Intron|TSSC4_ENST00000451491.2_Frame_Shift_Ins_p.G210fs	p.G210fs			Q9Y5U2	TSSC4_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)	3	1072_1073	+		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)	210					C9JS66|Q86VL2|Q9BRS6	Frame_Shift_Ins	INS	ENST00000333256.6	37	c.629_630insG	CCDS7735.1																																																																																				0.658	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		8	401						8	401	---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3720389	3720389	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:3720389delT	ENST00000324932.7	-	25	4352	c.3932delA	c.(3931-3933)aacfs	p.N1311fs	NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000488828.1_5'Flank	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1328					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CACAGGGCTGTTTTTTTGGGT	0.512			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																	ENST00000324932.7				Dom	yes		11	11p15	4928	T	nucleoporin 98kDa			L	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""		AML		0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66						c.(3931-3933)acfs		nucleoporin 98kDa							176.0	183.0	180.0					11																	3720389		2201	4298	6499	SO:0001589	frameshift_variant	4928				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity	g.chr11:3720389delT	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.3932delA	11.37:g.3720389delT	ENSP00000316032:p.Asn1311fs					NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs	p.N1311fs	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)	25	4352	-		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)	1328					Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	37	c.3932delA	CCDS7746.1																																																																																				0.512	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		14	1520						14	1520	---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9167317	9167317	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:9167317delC	ENST00000328194.3	-	17	3223	c.2903delG	c.(2902-2904)ggcfs	p.G968fs	DENND5A_ENST00000527700.1_Frame_Shift_Del_p.G311fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.G968fs	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	968	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GAACATGGAGCCCCCCAGCTT	0.478																																						ENST00000328194.3																			0				breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(2902-2904)gcfs		DENN/MADD domain containing 5A							292.0	284.0	287.0					11																	9167317		2201	4296	6497	SO:0001589	frameshift_variant	23258							g.chr11:9167317delC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2903delG	11.37:g.9167317delC	ENSP00000328524:p.Gly968fs					DENND5A_ENST00000527700.1_Frame_Shift_Del_p.G311fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.G968fs	p.G968fs	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN			17	3223	-			968			PLAT.		B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Frame_Shift_Del	DEL	ENST00000328194.3	37	c.2903delG	CCDS31423.1																																																																																				0.478	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		8	2136						8	2136	---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35313881	35313881	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:35313881delA	ENST00000278379.3	-	7	1326	c.1044delT	c.(1042-1044)tttfs	p.F348fs	SLC1A2_ENST00000395750.1_Frame_Shift_Del_p.F339fs|SLC1A2_ENST00000395753.1_Frame_Shift_Del_p.F339fs|SLC1A2_ENST00000606205.1_Frame_Shift_Del_p.F348fs	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	348					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			AAATGCCAGCAAAAAAGGAGA	0.468																																					NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	ENST00000278379.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24						c.(1042-1044)ttfs		solute carrier family 1 (glial high affinity glutamate transporter), member 2	L-Glutamic Acid(DB00142)						192.0	198.0	196.0					11																	35313881		2202	4298	6500	SO:0001589	frameshift_variant	6506				D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity	g.chr11:35313881delA	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.1044delT	11.37:g.35313881delA	ENSP00000278379:p.Phe348fs					SLC1A2_ENST00000395753.1_Frame_Shift_Del_p.F339fs|SLC1A2_ENST00000606205.1_Frame_Shift_Del_p.F348fs|SLC1A2_ENST00000395750.1_Frame_Shift_Del_p.F339fs	p.F348fs	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	STAD - Stomach adenocarcinoma(6;0.00731)		7	1326	-	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	348					B4DQE9|Q14417|Q541G6|U3KQQ4	Frame_Shift_Del	DEL	ENST00000278379.3	37	c.1044delT	CCDS31459.1																																																																																				0.468	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		7	1678						7	1678	---	---	---	---
RPLP0P2	113157	broad.mit.edu	37	11	61405017	61405019	+	RNA	DEL	CTG	CTG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:61405017_61405019delCTG	ENST00000496593.1	+	0	1621_1623					NR_002775.2				ribosomal protein, large, P0 pseudogene 2																		acagctgctcctgctgctgctgc	0.557																																						ENST00000496593.1																			0																																																			0							g.chr11:61405017_61405019delCTG	BC010523		11q12.2	2014-08-07			ENSG00000243742	ENSG00000243742		"""L ribosomal proteins"""	17960	pseudogene	pseudogene						19123937, 25089627	Standard	NR_002775		Approved		uc001nrz.1		OTTHUMG00000158396		11.37:g.61405026_61405028delCTG								NR_002775.2						0	1621_1623	+									RNA	DEL	ENST00000496593.1	37																																																																																						0.557	RPLP0P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000350911.1	NR_002775		9	194						9	194	---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62649529	62649529	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:62649529delA	ENST00000377890.2	+	5	1060	c.892delA	c.(892-894)aaafs	p.K300fs	SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000338663.7_Frame_Shift_Del_p.K199fs|SLC3A2_ENST00000535296.1_Frame_Shift_Del_p.K269fs|SLC3A2_ENST00000377891.2_Frame_Shift_Del_p.K301fs|SLC3A2_ENST00000377892.1_Frame_Shift_Del_p.K331fs|SLC3A2_ENST00000377889.2_Frame_Shift_Del_p.K238fs	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	300					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)	p.K331fs*31(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						GCAATCGGCTAAAAAAAAGAG	0.463																																						ENST00000377892.1																			1	Deletion - Frameshift(1)	p.K331fs*31(1)	ovary(1)	endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						c.(985-987)aafs		solute carrier family 3 (amino acid transporter heavy chain), member 2							73.0	74.0	74.0					11																	62649529		2201	4298	6499	SO:0001589	frameshift_variant	6520				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding	g.chr11:62649529delA		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.892delA	11.37:g.62649529delA	ENSP00000367122:p.Lys300fs					SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000535296.1_Frame_Shift_Del_p.K269fs|SLC3A2_ENST00000338663.7_Frame_Shift_Del_p.K199fs|SLC3A2_ENST00000377891.2_Frame_Shift_Del_p.K301fs|SLC3A2_ENST00000377889.2_Frame_Shift_Del_p.K238fs|SLC3A2_ENST00000377890.2_Frame_Shift_Del_p.K300fs	p.K331fs			P08195	4F2_HUMAN			6	1209	+			300					Q13543	Frame_Shift_Del	DEL	ENST00000377890.2	37	c.985delA	CCDS8039.2																																																																																				0.463	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		7	508						7	508	---	---	---	---
KRTAP5-7	440050	broad.mit.edu	37	11	71238416	71238436	+	In_Frame_Del	DEL	TGTGGCTCTGGCTGTGGGGGA	TGTGGCTCTGGCTGTGGGGGA	-	rs554986629|rs201675734|rs572895813	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:71238416_71238436delTGTGGCTCTGGCTGTGGGGGA	ENST00000398536.4	+	1	104_124	c.70_90delTGTGGCTCTGGCTGTGGGGGA	c.(70-90)tgtggctctggctgtgggggadel	p.CGSGCGG24del		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	24						keratin filament (GO:0045095)		p.G30G(1)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						CTGTGGGGGCTGTGGCTCTGGCTGTGGGGGATGTGGCTCCA	0.665																																						ENST00000398536.4																			1	Substitution - coding silent(1)	p.G30G(1)	kidney(1)	breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						c.(70-90)del		keratin associated protein 5-7																																				SO:0001651	inframe_deletion	440050					keratin filament		g.chr11:71238416_71238436delTGTGGCTCTGGCTGTGGGGGA	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.70_90delTGTGGCTCTGGCTGTGGGGGA	11.37:g.71238416_71238436delTGTGGCTCTGGCTGTGGGGGA	ENSP00000417330:p.Cys24_Gly30del						p.CGSGCGG24del	NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN			1	104_124	+			24					B2RNM3|Q701N5	In_Frame_Del	DEL	ENST00000398536.4	37	c.70_90delTGTGGCTCTGGCTGTGGGGGA	CCDS41682.1																																																																																				0.665	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			8	1479						8	1479	---	---	---	---
GDPD4	220032	broad.mit.edu	37	11	76928312	76928315	+	Splice_Site	DEL	ATCT	ATCT	-	rs373265622|rs538773767		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:76928312_76928315delATCT	ENST00000376217.2	-	17	1791_1792	c.1541_1542delAGAT	c.(1540-1542)aag>a	p.K514fs	GDPD4_ENST00000315938.4_3'UTR			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	514					glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						CTATGTGCAAatctatctatctat	0.471																																						ENST00000376217.2																			0				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						c.e17-1		glycerophosphodiester phosphodiesterase domain containing 4				0,120,4144		0,0,0,54,12,2066						-4.4	0.0			131	2,475,7777		0,0,2,232,11,3882	no	utr-3	GDPD4	NM_182833.1		0,0,2,286,23,5948	A1A1,A1A2,A1R,A2A2,A2R,RR		5.779,2.8143,4.7691				2,595,11921				SO:0001630	splice_region_variant	220032				glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding	g.chr11:76928312_76928315delATCT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1541-1AGAT>-	11.37:g.76928320_76928323delATCT						GDPD4_ENST00000315938.4_3'UTR	p.514_splice			Q6W3E5	GDPD4_HUMAN			17	1791_1792	-			514					Q7Z5B0	Splice_Site	DEL	ENST00000376217.2	37	c.1540_splice																																																																																					0.471	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	Frame_Shift_Del	9	427						9	427	---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89106662	89106663	+	Splice_Site	INS	-	-	A	rs548576417|rs552289081|rs56022003	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:89106662_89106663insA	ENST00000263317.4	-	12	1313		c.e12-2		NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000375979.3_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000532825.1_Splice_Site|NOX4_ENST00000534731.1_Splice_Site|NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000343727.5_Splice_Site|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000535633.1_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000525196.1_Intron			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_ENST00000375979.3_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000343727.5_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000263317.4_Splice_Site|NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000532825.1_Splice_Site|NOX4_ENST00000534731.1_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	13	690						13	690	---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102738793	102738794	+	RNA	INS	-	-	T	rs112457531|rs5794199|rs199886633|rs68192524		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:102738793_102738794insT	ENST00000532855.1	-	0	727_728							P39900	MMP12_HUMAN	matrix metallopeptidase 12 (macrophage elastase)						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|proteolysis (GO:0006508)|wound healing, spreading of epidermal cells (GO:0035313)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	26		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)|Marimastat(DB00786)	TGAGGAACAAGTGGTGCCTAAG	0.416																																						ENST00000532855.1																			0				autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	26								matrix metallopeptidase 12 (macrophage elastase)	Acetohydroxamic Acid(DB00551)																																					4321				positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding	g.chr11:102738793_102738794insT	L23808	CCDS73375.1	11q22.3	2009-02-26	2005-08-08			ENSG00000262406			7158	protein-coding gene	gene with protein product		601046	"""matrix metalloproteinase 12 (macrophage elastase)"""				Standard	NM_002426		Approved	HME	uc001phk.3	P39900			11.37:g.102738794_102738794dupT										P39900	MMP12_HUMAN		BRCA - Breast invasive adenocarcinoma(274;0.014)	0	727_728	-		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)						B2R9X8|B7ZLF6|Q2M1L9	RNA	INS	ENST00000532855.1	37																																																																																						0.416	MMP12-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000386646.1	NM_002426		7	58						7	58	---	---	---	---
CD3G	917	broad.mit.edu	37	11	118220583	118220583	+	Frame_Shift_Del	DEL	A	A	-	rs570768621|rs199676861	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:118220583delA	ENST00000532917.1	+	3	273	c.205delA	c.(205-207)aaafs	p.K71fs	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_Frame_Shift_Del_p.K11fs	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	71	Ig-like.				cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	AACTGAAGATAAAAAAAAATG	0.403													AAAAAAAAA|AAAAAAAAA|AAAAAAAA|deletion	3	0.000599042	0.0008	0.0014	5008	,	,		19811	0.0		0.001	False		,,,				2504	0.0					ENST00000532917.1																			0				breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	GRCh37	CM983819	CD3G	M		c.(205-207)aafs		CD3g molecule, gamma (CD3-TCR complex)							100.0	97.0	98.0					11																	118220583		2200	4296	6496	SO:0001589	frameshift_variant	917				establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity	g.chr11:118220583delA	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.205delA	11.37:g.118220583delA	ENSP00000431445:p.Lys71fs					CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_Frame_Shift_Del_p.K11fs	p.K71fs	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	3	273	+	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)	71			Ig-like.		Q2HIZ6	Frame_Shift_Del	DEL	ENST00000532917.1	37	c.205delA	CCDS8395.1																																																																																				0.403	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073		9	476						9	476	---	---	---	---
CCDC153	283152	broad.mit.edu	37	11	119061043	119061043	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:119061043delG	ENST00000503566.2	-	6	598	c.599delC	c.(598-600)cctfs	p.P200fs	CCDC153_ENST00000415318.1_Frame_Shift_Del_p.P200fs			Q494R4	CC153_HUMAN	coiled-coil domain containing 153	200										lung(3)|stomach(1)	4						CAAAGATCCAGGGGGGGTGAG	0.567																																						ENST00000503566.2																			0				lung(3)|stomach(1)	4						c.(598-600)ctfs		coiled-coil domain containing 153							92.0	88.0	89.0					11																	119061043		2200	4295	6495	SO:0001589	frameshift_variant	283152							g.chr11:119061043delG		CCDS44753.1	11q23.3	2011-07-22			ENSG00000248712	ENSG00000248712			27446	protein-coding gene	gene with protein product						12477932	Standard	NM_001145018		Approved	LOC283152	uc010rze.2	Q494R4	OTTHUMG00000156903	ENST00000503566.2:c.599delC	11.37:g.119061043delG	ENSP00000423567:p.Pro200fs					CCDC153_ENST00000415318.1_Frame_Shift_Del_p.P200fs	p.P200fs			Q494R4	CC153_HUMAN			6	598	-			200						Frame_Shift_Del	DEL	ENST00000503566.2	37	c.599delC	CCDS44753.1																																																																																				0.567	CCDC153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388331.2	NM_001033658		8	833						8	833	---	---	---	---
FAM118B	79607	broad.mit.edu	37	11	126131333	126131335	+	In_Frame_Del	DEL	AGA	AGA	-	rs138767340		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr11:126131333_126131335delAGA	ENST00000533050.1	+	8	1489_1491	c.996_998delAGA	c.(994-999)agagaa>aga	p.E333del	FAM118B_ENST00000529731.1_In_Frame_Del_p.E257del|FAM118B_ENST00000360194.4_In_Frame_Del_p.E332del	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	333										breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		GGATGGTGAGAGAAGGTCAGCTA	0.379																																						ENST00000533050.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13						c.(994-999)aga>ag		family with sequence similarity 118, member B				1,4263		0,1,2131						4.1	1.0			166	2,8252		0,2,4125	no	coding	FAM118B	NM_024556.3		0,3,6256	A1A1,A1R,RR		0.0242,0.0235,0.024				3,12515				SO:0001651	inframe_deletion	79607							g.chr11:126131333_126131335delAGA	BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.996_998delAGA	11.37:g.126131333_126131335delAGA	ENSP00000433343:p.Glu333del					FAM118B_ENST00000360194.4_In_Frame_Del_p.RE331del	p.RE332del	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)	8	1489_1491	+	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	332					Q9H7B0	In_Frame_Del	DEL	ENST00000533050.1	37	c.996_998delAGA	CCDS8470.1																																																																																				0.379	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		7	277						7	277	---	---	---	---
ACSM4	341392	broad.mit.edu	37	12	7456935	7456935	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:7456935delT	ENST00000399422.4	+	1	56	c.8delT	c.(7-9)attfs	p.I3fs		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	3					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						ACCATGAAGATTTTTTTCCGC	0.473																																						ENST00000399422.4																			0				endometrium(6)|kidney(1)|lung(14)	21						c.(7-9)atfs		acyl-CoA synthetase medium-chain family member 4							134.0	130.0	131.0					12																	7456935		1881	4115	5996	SO:0001589	frameshift_variant	341392				fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding	g.chr12:7456935delT		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"""Acyl-CoA synthetase family"""	32016	protein-coding gene	gene with protein product	"""similar to olfactory specific medium-chain acyl CoA synthetase"""	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.8delT	12.37:g.7456935delT	ENSP00000382349:p.Ile3fs						p.I3fs	NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN			1	56	+			3					A8MTI6	Frame_Shift_Del	DEL	ENST00000399422.4	37	c.8delT	CCDS44825.1																																																																																				0.473	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		7	1013						7	1013	---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13154583	13154583	+	5'Flank	DEL	G	G	-	rs398076428|rs59113920	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:13154583delG	ENST00000014930.4	-	0	0				RP11-377D9.3_ENST00000543321.1_lincRNA|HEBP1_ENST00000536942.1_5'Flank	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		TCTGCTGAGCGGGGGCCCCCG	0.731													GGGG|GGGGG|GGGG|insertion	2433	0.485823	0.3949	0.4986	5008	,	,		11429	0.378		0.6064	False		,,,				2504	0.5869					ENST00000543321.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr12:13154583delG	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771		12.37:g.13154583delG	Exception_encountered					HTR7P1_ENST00000535469.1_RNA								0	31	+								A8K1G2|Q9Y5Z5	RNA	DEL	ENST00000014930.4	37		CCDS31749.1																																																																																				0.731	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			9	17						9	17	---	---	---	---
SCAF11	9169	broad.mit.edu	37	12	46318575	46318577	+	In_Frame_Del	DEL	GGT	GGT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:46318575_46318577delGGT	ENST00000369367.3	-	12	4073_4075	c.3840_3842delACC	c.(3838-3843)ccaccc>ccc	p.1280_1281PP>P	SCAF11_ENST00000465950.1_In_Frame_Del_p.965_966PP>P|SCAF11_ENST00000549162.1_In_Frame_Del_p.1088_1089PP>P|SCAF11_ENST00000419565.2_In_Frame_Del_p.1280_1281PP>P|SCAF11_ENST00000550629.1_5'Flank	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1280	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TGGGGGAGGGGGTGGTGGTGGTG	0.483																																						ENST00000465950.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						c.(2893-2898)ccc>cc		SR-related CTD-associated factor 11																																				SO:0001651	inframe_deletion	9169				spliceosome assembly	nucleus	protein binding|zinc ion binding	g.chr12:46318575_46318577delGGT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.3840_3842delACC	12.37:g.46318584_46318586delGGT	ENSP00000358374:p.Pro1285del					SCAF11_ENST00000419565.2_In_Frame_Del_p.PP1284del|SCAF11_ENST00000549162.1_In_Frame_Del_p.PP1092del|SCAF11_ENST00000369367.3_In_Frame_Del_p.PP1284del	p.PP969del			Q99590	SCAFB_HUMAN			2	4104_4106	-			1284			Arg-rich.		A6NEU9|A6NLW5|Q8IW59	In_Frame_Del	DEL	ENST00000369367.3	37	c.2895_2897delACC	CCDS8748.2																																																																																				0.483	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		7	443						7	443	---	---	---	---
TUBA1A	7846	broad.mit.edu	37	12	49580272	49580274	+	Intron	DEL	GGA	GGA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:49580272_49580274delGGA	ENST00000295766.5	-	3	706				TUBA1A_ENST00000546918.1_In_Frame_Del_p.S116del|TUBA1A_ENST00000301071.7_Intron|TUBA1A_ENST00000550767.1_Intron	NM_001270399.1	NP_001257328.1	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a						'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			stomach(1)|upper_aerodigestive_tract(1)	2					Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570)	ggagcaggggggaggaggaggag	0.621																																					Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)	ENST00000546918.1																			0				stomach(1)|upper_aerodigestive_tract(1)	2						c.(346-348)del		tubulin, alpha 1a																																				SO:0001627	intron_variant	7846				'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|structural molecule activity	g.chr12:49580272_49580274delGGA	AF141347	CCDS8781.1, CCDS58226.1, CCDS58227.1	12q13.12	2007-02-07						"""Tubulins"""	20766	protein-coding gene	gene with protein product	"""tubulin, alpha, brain-specific"""	602529				11504633, 3839072	Standard	NM_006009		Approved	TUBA3, B-ALPHA-1, FLJ25113	uc010smg.1	Q71U36	OTTHUMG00000169511	ENST00000295766.5:c.227-31TCC>-	12.37:g.49580281_49580283delGGA						TUBA1A_ENST00000550767.1_Intron|TUBA1A_ENST00000295766.5_Intron|TUBA1A_ENST00000301071.7_Intron	p.S116del			Q71U36	TBA1A_HUMAN			2	432_434	-			0					A8K0B8|G3V1U9|P04687|P05209	In_Frame_Del	DEL	ENST00000295766.5	37	c.346_348delTCC	CCDS58227.1																																																																																				0.621	TUBA1A-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404547.2	NM_006009		7	475						7	475	---	---	---	---
PRPF40B	25766	broad.mit.edu	37	12	50025258	50025258	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:50025258delC	ENST00000380281.1	+	2	157	c.93delC	c.(91-93)atcfs	p.I31fs	PRPF40B_ENST00000261897.1_Frame_Shift_Del_p.I25fs|PRPF40B_ENST00000548825.2_Frame_Shift_Del_p.I53fs			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	31	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						CACCAGCTATCCCCCCCATGC	0.607																																						ENST00000261897.1																			0				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						c.(73-75)atfs		PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)							84.0	87.0	86.0					12																	50025258		2203	4300	6503	SO:0001589	frameshift_variant	25766				mRNA processing|RNA splicing	nuclear speck		g.chr12:50025258delC	AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"""Huntingtin interacting protein C"""		"""PRP40 pre-mRNA processing factor 40 homolog B (yeast)"""			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.93delC	12.37:g.50025258delC	ENSP00000369634:p.Ile31fs					PRPF40B_ENST00000548825.2_Frame_Shift_Del_p.I53fs|PRPF40B_ENST00000380281.1_Frame_Shift_Del_p.I31fs	p.I25fs			Q6NWY9	PR40B_HUMAN			2	626	+			31			Pro-rich.		O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Frame_Shift_Del	DEL	ENST00000380281.1	37	c.75delC																																																																																					0.607	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		7	1028						7	1028	---	---	---	---
OR10A7	121364	broad.mit.edu	37	12	55615114	55615116	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:55615114_55615116delCTT	ENST00000326258.1	+	1	306_308	c.306_308delCTT	c.(304-309)tacttc>tac	p.F107del		NM_001005280.1	NP_001005280.1	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A, member 7	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3)	24						CCCAGATGTACTTCTTCTTCTTC	0.414																																						ENST00000326258.1																			0				endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3)	24						c.(304-309)tac>ta		olfactory receptor, family 10, subfamily A, member 7																																				SO:0001651	inframe_deletion	121364				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr12:55615114_55615116delCTT	BK004327	CCDS31815.1	12q13.13	2012-08-09				ENSG00000179919		"""GPCR / Class A : Olfactory receptors"""	15329	protein-coding gene	gene with protein product							Standard	NM_001005280		Approved		uc010spf.2	Q8NGE5	OTTHUMG00000169860	ENST00000326258.1:c.306_308delCTT	12.37:g.55615123_55615125delCTT	ENSP00000326718:p.Phe107del						p.YF102del	NM_001005280.1	NP_001005280.1	Q8NGE5	O10A7_HUMAN			1	306_308	+			102					Q6IFD5|Q96R19	In_Frame_Del	DEL	ENST00000326258.1	37	c.306_308delCTT	CCDS31815.1																																																																																				0.414	OR10A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406308.1			8	1193						8	1193	---	---	---	---
OR6C75	390323	broad.mit.edu	37	12	55759486	55759486	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:55759486delT	ENST00000343399.3	+	1	592	c.592delT	c.(592-594)tttfs	p.F199fs		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	199						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L200fs*1(1)		endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						ACTCATGGCATTTTTTTTAGC	0.393																																						ENST00000343399.3																			1	Deletion - Frameshift(1)	p.L200fs*1(1)	large_intestine(1)	endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						c.(592-594)ttfs		olfactory receptor, family 6, subfamily C, member 75							154.0	133.0	140.0					12																	55759486		2203	4300	6503	SO:0001589	frameshift_variant	390323				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr12:55759486delT		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"""GPCR / Class A : Olfactory receptors"""	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.592delT	12.37:g.55759486delT	ENSP00000368987:p.Phe199fs						p.F199fs	NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN			1	592	+			199						Frame_Shift_Del	DEL	ENST00000343399.3	37	c.592delT	CCDS31820.1																																																																																				0.393	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			7	539						7	539	---	---	---	---
RP11-74M13.4	0	broad.mit.edu	37	12	57255299	57255300	+	RNA	INS	-	-	A	rs139092727	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:57255299_57255300insA	ENST00000557452.1	+	0	720				SNORA48_ENST00000391081.1_RNA																							ATGGAAGAAGGAAaaaaaaata	0.426													AAAAAAAAA|AAAAAAAAA|AAAAAAAAAA|insertion	26	0.00519169	0.0182	0.0	5008	,	,		18782	0.0		0.001	False		,,,				2504	0.001					ENST00000557452.1																			0																																																			0							g.chr12:57255299_57255300insA																													12.37:g.57255308_57255308dupA														0	720	+									RNA	INS	ENST00000557452.1	37																																																																																						0.426	RP11-74M13.4-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000410896.1			7	228						7	228	---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57674205	57674207	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:57674205_57674207delTGC	ENST00000347140.3	-	14	1626_1628	c.1236_1238delGCA	c.(1234-1239)cagcaa>caa	p.412_413QQ>Q	R3HDM2_ENST00000441731.2_In_Frame_Del_p.73_74QQ>Q|R3HDM2_ENST00000403821.2_In_Frame_Del_p.412_413QQ>Q|R3HDM2_ENST00000402412.1_In_Frame_Del_p.426_427QQ>Q|R3HDM2_ENST00000413953.2_In_Frame_Del_p.139_140QQ>Q|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000358907.2_In_Frame_Del_p.412_413QQ>Q			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	412	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						AGCAGGAAGTtgctgctgctgct	0.576																																						ENST00000402412.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						c.(1276-1281)caa>ca		R3H domain containing 2																																				SO:0001651	inframe_deletion	22864					nucleus	nucleic acid binding	g.chr12:57674205_57674207delTGC	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1236_1238delGCA	12.37:g.57674214_57674216delTGC	ENSP00000317903:p.Gln413del					RP11-123K3.4_ENST00000548184.1_RNA|R3HDM2_ENST00000358907.2_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000393811.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000441731.2_In_Frame_Del_p.QQ73del|R3HDM2_ENST00000347140.3_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000413953.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000403821.2_In_Frame_Del_p.QQ412del	p.QQ426del			Q9Y2K5	R3HD2_HUMAN			14	1668_1670	-			412			Gln-rich.		Q2M1T9|Q3ZCT5	In_Frame_Del	DEL	ENST00000347140.3	37	c.1278_1280delGCA	CCDS8937.2																																																																																				0.576	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		15	599						15	599	---	---	---	---
LRIG3	121227	broad.mit.edu	37	12	59268350	59268351	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:59268350_59268351insG	ENST00000320743.3	-	17	2986_2987	c.2700_2701insC	c.(2698-2703)acctgcfs	p.C901fs	LRIG3_ENST00000379141.4_Frame_Shift_Ins_p.C841fs	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	901					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TCAATATGGCAGGTCCCTTTGA	0.401			T	ROS1	NSCLC																																	ENST00000320743.3				Dom	yes		12	12q14.1	121227	T	leucine-rich repeats and immunoglobulin-like domains 3			E	ROS1		NSCLC	LRIG3/ROS1(2)	0				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						c.(2698-2703)acgccafs		leucine-rich repeats and immunoglobulin-like domains 3																																				SO:0001589	frameshift_variant	121227					integral to membrane		g.chr12:59268350_59268351insG	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2701dupC	12.37:g.59268352_59268352dupG	ENSP00000326759:p.Cys901fs					LRIG3_ENST00000379141.4_Frame_Shift_Ins_p.P841fs	p.P901fs	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	GBM - Glioblastoma multiforme(1;1.17e-18)		17	2986_2987	-			901					Q6UXL7|Q8NC72	Frame_Shift_Ins	INS	ENST00000320743.3	37	c.2700_2701insC	CCDS8960.1																																																																																				0.401	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		9	486						9	486	---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72057256	72057258	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:72057256_72057258delGCT	ENST00000378743.3	-	1	491_493	c.133_135delAGC	c.(133-135)agcdel	p.S45del	THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000548100.1_In_Frame_Del_p.S45del|ZFC3H1_ENST00000552037.1_In_Frame_Del_p.S45del|ZFC3H1_ENST00000549407.1_5'Flank|THAP2_ENST00000547843.1_5'Flank	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	45	Ser-rich.				RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GCCCGCCGCCGCTGCTGCTGCTG	0.631											OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000378743.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(133-135)del		zinc finger, C3H1-type containing				2,34,3866		0,0,2,4,26,1919						4.0	1.0			58	1,83,7932		0,0,1,9,65,3933	no	codingComplex	ZFC3H1	NM_144982.4		0,0,3,13,91,5852	A1A1,A1A2,A1R,A2A2,A2R,RR		1.0479,0.9226,1.0069				3,117,11798				SO:0001651	inframe_deletion	196441				RNA processing	intracellular	metal ion binding	g.chr12:72057256_72057258delGCT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.133_135delAGC	12.37:g.72057265_72057267delGCT	ENSP00000368017:p.Ser45del		OREG0021993	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1134	THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000548100.1_In_Frame_Del_p.S45del|ZFC3H1_ENST00000552037.1_In_Frame_Del_p.S45del	p.S45del	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN			1	491_493	-			45			Ser-rich.		Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	In_Frame_Del	DEL	ENST00000378743.3	37	c.133_135delAGC	CCDS41813.1																																																																																				0.631	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		16	907						16	907	---	---	---	---
RP11-114H23.1	0	broad.mit.edu	37	12	76082490	76082491	+	lincRNA	INS	-	-	T	rs71276351		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:76082490_76082491insT	ENST00000552856.1	-	0	401				SNORA70_ENST00000516084.2_RNA																							cattctTTTTCTTTTTTTTTTT	0.361																																						ENST00000552856.1																			0																																																			0							g.chr12:76082490_76082491insT																													12.37:g.76082501_76082501dupT														0	401	-									RNA	INS	ENST00000552856.1	37																																																																																						0.361	RP11-114H23.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000405775.2			13	18						13	18	---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111785948	111785948	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:111785948delC	ENST00000261726.6	+	22	4434	c.4280delC	c.(4279-4281)gccfs	p.A1427fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1427	Pro-rich.				cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCACCTGGCGCCCCCCCTGCC	0.657																																						ENST00000261726.6																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						c.(4279-4281)gcfs		cut-like homeobox 2							45.0	53.0	50.0					12																	111785948		2032	4169	6201	SO:0001589	frameshift_variant	23316					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr12:111785948delC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.4280delC	12.37:g.111785948delC	ENSP00000261726:p.Ala1427fs						p.A1427fs	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN			22	4434	+			1427			Pro-rich.		A7E2Y4	Frame_Shift_Del	DEL	ENST00000261726.6	37	c.4280delC	CCDS41837.1																																																																																				0.657	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		7	728						7	728	---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120595737	120595739	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr12:120595737_120595739delCTC	ENST00000300648.6	-	26	3013_3015	c.3001_3003delGAG	c.(3001-3003)gagdel	p.E1001del	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1001					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGGCCATCCACTCCTCCTCCTCC	0.631																																						ENST00000300648.6																			0				NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94						c.(3001-3003)del		GCN1 general control of amino-acid synthesis 1-like 1 (yeast)																																				SO:0001651	inframe_deletion	10985				regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding	g.chr12:120595737_120595739delCTC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3001_3003delGAG	12.37:g.120595746_120595748delCTC	ENSP00000300648:p.Glu1001del						p.E1001del	NM_006836.1	NP_006827.1	Q92616	GCN1L_HUMAN			26	3013_3015	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		1001					A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	In_Frame_Del	DEL	ENST00000300648.6	37	c.3001_3003delGAG	CCDS41847.1																																																																																				0.631	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			9	335						9	335	---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20426143	20426145	+	In_Frame_Del	DEL	CAT	CAT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:20426143_20426145delCAT	ENST00000337963.4	-	3	440_442	c.176_178delATG	c.(175-180)gatgtt>gtt	p.D59del	ZMYM5_ENST00000382905.4_In_Frame_Del_p.D59del|ZMYM5_ENST00000382907.4_In_Frame_Del_p.D59del	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	59	Poly-Asp.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ATAAACACAAcatcatcatcatc	0.379																																						ENST00000337963.4																			0				kidney(1)|large_intestine(5)|lung(9)	15						c.(175-180)gtt>g		zinc finger, MYM-type 5																																				SO:0001651	inframe_deletion	9205					nucleus	zinc ion binding	g.chr13:20426143_20426145delCAT	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.176_178delATG	13.37:g.20426152_20426154delCAT	ENSP00000337034:p.Asp59del					ZMYM5_ENST00000382907.4_In_Frame_Del_p.DV59del|ZMYM5_ENST00000382905.4_In_Frame_Del_p.DV59del	p.DV59del	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)	3	440_442	-		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)	59			Poly-Asp.		B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	In_Frame_Del	DEL	ENST00000337963.4	37	c.176_178delATG																																																																																					0.379	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		8	495						8	495	---	---	---	---
TPTE2P6	374491	broad.mit.edu	37	13	25157747	25157748	+	RNA	INS	-	-	T	rs74332804		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:25157747_25157748insT	ENST00000453498.1	+	0	554				TPTE2P6_ENST00000440905.1_RNA																							AAAATGGGAGGTTTTTTTAGGG	0.411																																						ENST00000453498.1																			0																																																			0							g.chr13:25157747_25157748insT																													13.37:g.25157754_25157754dupT														0	554	+									RNA	INS	ENST00000453498.1	37																																																																																						0.411	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			7	75						7	75	---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27255386	27255387	+	Frame_Shift_Ins	INS	-	-	C	rs529756888|rs141429361	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:27255386_27255387insC	ENST00000335327.5	+	8	1090_1091	c.912_913insC	c.(913-915)cccfs	p.P305fs	WASF3_ENST00000361042.4_Frame_Shift_Ins_p.P302fs	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	305	Poly-Pro.				actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CTCAGCAGCCGCCCCCCCCGCC	0.678																																						ENST00000361042.4																			0				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22						c.(901-906)ccccccfs		WAS protein family, member 3				82,4062		3,76,1993						-6.7	0.1			31	128,8010		7,114,3948	no	frameshift	WASF3	NM_006646.5		10,190,5941	A1A1,A1R,RR		1.5729,1.9788,1.7098				210,12072				SO:0001589	frameshift_variant	10810				actin filament polymerization	cytoplasm|cytoskeleton	actin binding	g.chr13:27255386_27255387insC	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.920dupC	13.37:g.27255394_27255394dupC	ENSP00000335055:p.Pro305fs					WASF3_ENST00000335327.5_Frame_Shift_Ins_p.PP304fs	p.PP301fs			Q9UPY6	WASF3_HUMAN		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)	8	1128_1129	+	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)	304					O94974|Q86VQ2	Frame_Shift_Ins	INS	ENST00000335327.5	37	c.903_904insC	CCDS9318.1																																																																																				0.678	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			9	513						9	513	---	---	---	---
GPALPP1	55425	broad.mit.edu	37	13	45580365	45580367	+	In_Frame_Del	DEL	GAT	GAT	-	rs138421508		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:45580365_45580367delGAT	ENST00000379151.4	+	3	353_355	c.250_252delGAT	c.(250-252)gatdel	p.D88del	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000357537.3_De_novo_Start_InFrame|GPALPP1_ENST00000361121.2_In_Frame_Del_p.D88del	NM_018559.2	NP_061029.2	Q8IXQ4	GPAM1_HUMAN	GPALPP motifs containing 1	88	Poly-Asp.																Ggatgatgacgatgatgatgatg	0.335																																						ENST00000361121.2																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|prostate(2)|skin(1)	12						c.(250-252)del						311,3953		154,3,1975						-7.1	0.0			182	654,7600		325,4,3798	no	coding	KIAA1704	NM_018559.2		479,7,5773	A1A1,A1R,RR		7.9234,7.2936,7.7089				965,11553				SO:0001651	inframe_deletion	0							g.chr13:45580365_45580367delGAT	AB051491	CCDS9394.1	13q14.12	2013-08-13	2013-08-12	2013-08-12	ENSG00000133114	ENSG00000133114			20298	protein-coding gene	gene with protein product			"""KIAA1704"""	KIAA1704		11214970	Standard	NM_018559		Approved	bA245H20.2, AD029, LSR7	uc001uzq.3	Q8IXQ4	OTTHUMG00000016841	ENST00000379151.4:c.250_252delGAT	13.37:g.45580374_45580376delGAT	ENSP00000368447:p.Asp88del					RP11-321C24.1_ENST00000437748.2_lincRNA|KIAA1704_ENST00000357537.3_De_novo_Start_InFrame|KIAA1704_ENST00000379151.4_In_Frame_Del_p.D88del	p.D88del			Q8IXQ4	K1704_HUMAN	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000313)|BRCA - Breast invasive adenocarcinoma(63;0.126)	3	285_287	+		Lung NSC(96;0.00143)|Prostate(109;0.0137)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	88			Poly-Asp.		A8K8X8|Q05BX8|Q05D87|Q5T3Z3|Q5T3Z5|Q9C0F9|Q9H2R0|Q9P0W6	In_Frame_Del	DEL	ENST00000379151.4	37	c.250_252delGAT	CCDS9394.1																																																																																				0.335	GPALPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044749.2	NM_018559		13	1286						13	1286	---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73357634	73357634	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:73357634delA	ENST00000326291.6	+	2	365	c.27delA	c.(25-27)tcafs	p.S9fs	DIS3_ENST00000545453.1_5'Flank|DIS3_ENST00000377780.4_5'Flank|DIS3_ENST00000475871.1_5'Flank|DIS3_ENST00000377767.4_5'Flank	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	9						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		CAAAGGAGTCAAAAAAAGTGA	0.303																																						ENST00000326291.6																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24						c.(25-27)tcfs		progesterone immunomodulatory binding factor 1							54.0	58.0	57.0					13																	73357634		2203	4300	6503	SO:0001589	frameshift_variant	10464					centrosome		g.chr13:73357634delA	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"""progesterone-induced blocking factor 1"""	607532	"""chromosome 13 open reading frame 24"""	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.27delA	13.37:g.73357634delA	ENSP00000317144:p.Ser9fs						p.S9fs	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN		GBM - Glioblastoma multiforme(99;0.000664)	2	365	+		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)	9					O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Frame_Shift_Del	DEL	ENST00000326291.6	37	c.27delA	CCDS31991.1																																																																																				0.303	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		8	501						8	501	---	---	---	---
SLITRK5	26050	broad.mit.edu	37	13	88330019	88330021	+	In_Frame_Del	DEL	GCA	GCA	-	rs552694563	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr13:88330019_88330021delGCA	ENST00000325089.6	+	2	2595_2597	c.2376_2378delGCA	c.(2374-2379)ctgcag>ctg	p.Q797del	SLITRK5_ENST00000400028.3_In_Frame_Del_p.Q556del	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	797					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					ACCACCACCTgcagcagcagcag	0.655																																						ENST00000325089.6																			0				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81						c.(2374-2379)ctg>ct		SLIT and NTRK-like family, member 5																																				SO:0001651	inframe_deletion	26050					integral to membrane		g.chr13:88330019_88330021delGCA	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.2376_2378delGCA	13.37:g.88330028_88330030delGCA	ENSP00000366283:p.Gln797del					SLITRK5_ENST00000400028.3_In_Frame_Del_p.LQ551del	p.LQ792del	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN			2	2595_2597	+	all_neural(89;0.101)|Medulloblastoma(90;0.163)		792					B3KNB8|B4DSH5|Q5VT81	In_Frame_Del	DEL	ENST00000325089.6	37	c.2376_2378delGCA	CCDS9465.1																																																																																				0.655	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			8	395						8	395	---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20852647	20852647	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:20852647delC	ENST00000262715.5	-	23	3282	c.3242delG	c.(3241-3243)ggtfs	p.G1081fs	TEP1_ENST00000545983.1_5'Flank|TEP1_ENST00000556935.1_Frame_Shift_Del_p.G973fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1081					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.V1082fs*47(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGCTGCCACACCCCCCCACTC	0.587																																						ENST00000262715.5																			1	Insertion - Frameshift(1)	p.V1082fs*47(1)	large_intestine(1)	NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96						c.(3241-3243)gtfs		telomerase-associated protein 1							108.0	128.0	121.0					14																	20852647		2203	4300	6503	SO:0001589	frameshift_variant	7011				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding	g.chr14:20852647delC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3242delG	14.37:g.20852647delC	ENSP00000262715:p.Gly1081fs					TEP1_ENST00000556935.1_Frame_Shift_Del_p.G973fs	p.G1081fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)	23	3282	-	all_cancers(95;0.00123)	all_lung(585;0.235)	1081					A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	37	c.3242delG	CCDS9548.1																																																																																				0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		11	1445						11	1445	---	---	---	---
CHD8	57680	broad.mit.edu	37	14	21884031	21884031	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:21884031delT	ENST00000557364.1	-	6	2015	c.1752delA	c.(1750-1752)aaafs	p.K584fs	CHD8_ENST00000430710.3_Frame_Shift_Del_p.K305fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Frame_Shift_Del_p.K584fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	584					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CCTCTGTATATTTTTTTCGCT	0.398																																						ENST00000399982.2																			0				NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85						c.(1750-1752)aafs		chromodomain helicase DNA binding protein 8							202.0	190.0	194.0					14																	21884031		1845	4090	5935	SO:0001589	frameshift_variant	57680				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding	g.chr14:21884031delT	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.1752delA	14.37:g.21884031delT	ENSP00000451601:p.Lys584fs					CHD8_ENST00000557364.1_Frame_Shift_Del_p.K584fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Frame_Shift_Del_p.K305fs	p.K584fs	NM_001170629.1	NP_001164100.1	Q9HCK8	CHD8_HUMAN	Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)	5	1816	-	all_cancers(95;0.00121)		584					Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	c.1752delA	CCDS53885.1																																																																																				0.398	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		7	899						7	899	---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39746242	39746243	+	Frame_Shift_Ins	INS	-	-	T	rs75842899|rs78536283	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:39746242_39746243insT	ENST00000280083.3	+	2	482_483	c.168_169insT	c.(169-171)tttfs	p.F57fs	RP11-407N17.3_ENST00000603904.1_Frame_Shift_Ins_p.F28fs|CTAGE5_ENST00000556148.1_Intron|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Ins_p.F592fs|CTAGE5_ENST00000396158.2_Frame_Shift_Ins_p.F57fs|CTAGE5_ENST00000341502.5_Frame_Shift_Ins_p.F57fs|CTAGE5_ENST00000396165.4_Frame_Shift_Ins_p.F28fs|CTAGE5_ENST00000553352.1_Frame_Shift_Ins_p.F28fs|CTAGE5_ENST00000348007.3_Frame_Shift_Ins_p.F57fs|CTAGE5_ENST00000341749.3_Frame_Shift_Ins_p.F45fs|CTAGE5_ENST00000557038.1_5'UTR			O15320	CTGE5_HUMAN	CTAGE family, member 5	57					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TTGCTGTTCTCTTTTTTTTGTG	0.371																																						ENST00000553728.1																			0											c.(1771-1776)ctttttfs																																						SO:0001589	frameshift_variant	0							g.chr14:39746242_39746243insT	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.176dupT	14.37:g.39746250_39746250dupT	ENSP00000280083:p.Phe57fs					CTAGE5_ENST00000280083.3_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000557038.1_5'UTR|CTAGE5_ENST00000348007.3_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000556148.1_Intron|CTAGE5_ENST00000396158.2_Frame_Shift_Ins_p.LF56fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000396165.4_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000553352.1_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000341502.5_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000341749.3_Frame_Shift_Ins_p.LF44fs	p.LF591fs							6	1986_1987	+								B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Ins	INS	ENST00000280083.3	37	c.1773_1774insT	CCDS9674.1																																																																																				0.371	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		12	391						12	391	---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71275774	71275776	+	In_Frame_Del	DEL	CCT	CCT	-	rs397840789|rs201322413		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:71275774_71275776delCCT	ENST00000554752.2	-	1	112_114	c.113_115delAGG	c.(112-117)gaggcg>gcg	p.E38del	MAP3K9_ENST00000555993.2_In_Frame_Del_p.E38del|MAP3K9_ENST00000381250.4_In_Frame_Del_p.E38del|RP6-65G23.3_ENST00000557691.1_lincRNA	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	38	Ala-rich.|Poly-Glu.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.E38delE(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCCGCCGCCGcctcctcctcctc	0.773																																					GBM(114;411 1587 13539 28235 50070)	ENST00000554752.2																			1	Deletion - In frame(1)	p.E38delE(1)	ovary(1)	breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46						c.(112-117)gcg>g		mitogen-activated protein kinase kinase kinase 9																																				SO:0001651	inframe_deletion	4293				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity	g.chr14:71275774_71275776delCCT	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.113_115delAGG	14.37:g.71275783_71275785delCCT	ENSP00000451612:p.Glu38del					MAP3K9_ENST00000555993.2_In_Frame_Del_p.EA38del|MAP3K9_ENST00000381250.4_In_Frame_Del_p.EA38del	p.EA38del			P80192	M3K9_HUMAN		all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)	1	112_114	-			38			Ala-rich.|Poly-Glu.		A3KN85|Q0D2G7|Q6EH31|Q9H2N5	In_Frame_Del	DEL	ENST00000554752.2	37	c.113_115delAGG																																																																																					0.773	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			7	32						7	32	---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72190482	72190484	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:72190482_72190484delTCC	ENST00000555818.1	+	16	4738_4740	c.4390_4392delTCC	c.(4390-4392)tccdel	p.S1468del	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_In_Frame_Del_p.S1447del|SIPA1L1_ENST00000381232.3_In_Frame_Del_p.S1447del|SIPA1L1_ENST00000537413.1_In_Frame_Del_p.S922del	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1468	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		ctcctcctcttcctcctcctcct	0.552																																						ENST00000555818.1																			0				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78						c.(4390-4392)del		signal-induced proliferation-associated 1 like 1																																				SO:0001651	inframe_deletion	26037				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity	g.chr14:72190482_72190484delTCC	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4390_4392delTCC	14.37:g.72190491_72190493delTCC	ENSP00000450832:p.Ser1468del					SIPA1L1_ENST00000537413.1_In_Frame_Del_p.S922del|SIPA1L1_ENST00000358550.2_In_Frame_Del_p.S1447del|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_In_Frame_Del_p.S1447del	p.S1468del	NM_015556.1	NP_056371.1	O43166	SI1L1_HUMAN		all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)	16	4738_4740	+			1468			Ser-rich.		J3KP19|O95321|Q9UDU4|Q9UNU4	In_Frame_Del	DEL	ENST00000555818.1	37	c.4390_4392delTCC	CCDS9807.1																																																																																				0.552	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		9	829						9	829	---	---	---	---
INF2	64423	broad.mit.edu	37	14	105174270	105174271	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr14:105174270_105174271insG	ENST00000392634.4	+	8	1778_1779	c.1666_1667insG	c.(1666-1668)cggfs	p.R556fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.R556fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	556	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CAGCCATCGGCGGGTGAACCCA	0.663																																						ENST00000392634.4																			0				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						c.(1666-1668)ggtfs		inverted formin, FH2 and WH2 domain containing																																				SO:0001589	frameshift_variant	64423				actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding	g.chr14:105174270_105174271insG	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1669dupG	14.37:g.105174273_105174273dupG	ENSP00000376410:p.Arg556fs					INF2_ENST00000330634.7_Frame_Shift_Ins_p.G556fs	p.G556fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)	8	1778_1779	+		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	556			FH2.		Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	37	c.1666_1667insG	CCDS9989.2																																																																																				0.663	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		13	356						13	356	---	---	---	---
SNHG14	104472715	broad.mit.edu	37	15	25324325	25324325	+	RNA	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:25324325delT	ENST00000546682.1	+	0	0				SNORD116-12_ENST00000384468.1_RNA|SNORD116-15_ENST00000384445.1_RNA|SNORD116-13_ENST00000384408.1_RNA|SNORD116-14_ENST00000383894.1_RNA|SNHG14_ENST00000549804.2_RNA	NR_003361.1				small nucleolar RNA host gene 14 (non-protein coding)																		ACAACTGTCATTTTTTTTGAT	0.478																																						ENST00000549804.2																			0																	12,2458		5,2,1228	82.0	80.0	80.0			0.2	0.1	15		82	18,4858		8,2,2428	no	intergenic				13,4,3656	A1A1,A1R,RR		0.3692,0.4858,0.4084			25324325	30,7316	876	1991	2867			0							g.chr15:25324325delT			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25324325delT														0	1377	+									RNA	DEL	ENST00000546682.1	37																																																																																						0.478	SNHG14-022	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000408281.1			8	386						8	386	---	---	---	---
SNHG14	104472715	broad.mit.edu	37	15	25432666	25432666	+	RNA	DEL	G	G	-	rs368646014		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:25432666delG	ENST00000424208.1	+	0	761				SNORD115-10_ENST00000365073.1_RNA|SNORD115-11_ENST00000363616.1_RNA|SNHG14_ENST00000414175.1_RNA|SNORD115-9_ENST00000362912.1_RNA	NR_003305.1				small nucleolar RNA host gene 14 (non-protein coding)																		TGTGTGTGGTGGGGGGTGCCC	0.552																																						ENST00000424208.1																			0																				277.0	278.0	278.0					15																	25432666		876	1991	2867			0							g.chr15:25432666delG			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25432666delG								NR_003305.1						0	761	+									RNA	DEL	ENST00000424208.1	37																																																																																						0.552	SNHG14-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000126729.2			8	1698						8	1698	---	---	---	---
HERC2P9	440248	broad.mit.edu	37	15	28913367	28913367	+	RNA	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:28913367delT	ENST00000528584.1	+	0	1224					NR_036443.1				hect domain and RLD 2 pseudogene 9																		TGAGTTCTCCTTTTTTTTTTT	0.308																																						ENST00000528584.1																			0																																																			0							g.chr15:28913367delT	BC047911		15q13.1	2011-05-24			ENSG00000206149	ENSG00000206149			30495	pseudogene	pseudogene							Standard	NR_036443		Approved	FLJ59185	uc010azc.3		OTTHUMG00000167114		15.37:g.28913367delT								NR_036443.1						0	1224	+									RNA	DEL	ENST00000528584.1	37																																																																																						0.308	HERC2P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000393268.1	NR_036443		8	45						8	45	---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57744359	57744360	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:57744359_57744360delAG	ENST00000281282.5	+	6	2004_2005	c.1926_1927delAG	c.(1924-1929)gaagagfs	p.EE642fs		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	642						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		ACATTAAAGAAGAGAGAGAGAG	0.441																																						ENST00000281282.5																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60						c.(1924-1929)gaagfs		cingulin-like 1																																				SO:0001589	frameshift_variant	84952					myosin complex|tight junction	motor activity	g.chr15:57744359_57744360delAG	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1926_1927delAG	15.37:g.57744369_57744370delAG	ENSP00000281282:p.Glu642fs						p.EE642fs	NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN		all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)	6	2004_2005	+			642					Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Frame_Shift_Del	DEL	ENST00000281282.5	37	c.1926_1927delAG	CCDS10161.1																																																																																				0.441	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		9	406						9	406	---	---	---	---
ICE2	79664	broad.mit.edu	37	15	60745782	60745782	+	Frame_Shift_Del	DEL	A	A	-	rs181931922	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:60745782delA	ENST00000561114.1	-	9	1307	c.1145delT	c.(1144-1146)ttcfs	p.F382fs	NARG2_ENST00000439632.1_Intron|NARG2_ENST00000261520.4_Intron	NM_001276385.1	NP_001263314.1														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						CCCTTAGGGGAAAAAAAAAGC	0.338																																						ENST00000561114.1																			0				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						c.(1144-1146)tcfs		NMDA receptor regulated 2							50.0	51.0	51.0					15																	60745782		2203	4297	6500	SO:0001589	frameshift_variant	79664					nucleus		g.chr15:60745782delA																												ENST00000561114.1:c.1145delT	15.37:g.60745782delA	ENSP00000454162:p.Phe382fs					NARG2_ENST00000261520.4_Intron|NARG2_ENST00000439632.1_Intron	p.F382fs	NM_001276385.1	NP_001263314.1	Q659A1	NARG2_HUMAN			9	1307	-			0						Frame_Shift_Del	DEL	ENST00000561114.1	37	c.1145delT																																																																																					0.338	NARG2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000416605.1			10	213						10	213	---	---	---	---
UBE2Q2P1	388165	broad.mit.edu	37	15	85077360	85077360	+	RNA	DEL	A	A	-	rs376357384	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:85077360delA	ENST00000339094.1	-	0	1678					NR_003661.2				ubiquitin-conjugating enzyme E2Q family member 2 pseudogene 1																		tttttaaactaaaaaaaaaaa	0.373													|||unknown(NO_COVERAGE)	2110	0.421326	0.4274	0.4049	5008	,	,		13748	0.4395		0.4095	False		,,,				2504	0.4182					ENST00000339094.1																			0																																																			0							g.chr15:85077360delA			15q25.2	2013-11-05	2009-12-17	2009-12-17	ENSG00000189136	ENSG00000189136			37439	pseudogene	pseudogene			"""ubiquitin-conjugating enzyme E2Q family pseudogene 1"""	UBE2QP1			Standard	NR_003661		Approved	FLJ43276	uc002bkn.1		OTTHUMG00000148662		15.37:g.85077360delA								NR_003661.2						0	1678	-									RNA	DEL	ENST00000339094.1	37																																																																																						0.373	UBE2Q2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000308970.2	NR_003661		13	55						13	55	---	---	---	---
DNM1P47	100216544	broad.mit.edu	37	15	102292783	102292786	+	RNA	DEL	CTCA	CTCA	-	rs61084368|rs143389223	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr15:102292783_102292786delCTCA	ENST00000561463.1	+	0	829_832									DNM1 pseudogene 47									p.Q125E(1)									GATGCTGCTTCTCAGAGCTGCTGT	0.603														1404	0.280351	0.2383	0.2939	5008	,	,		40661	0.3135		0.2406	False		,,,				2504	0.3344					ENST00000561463.1																			1	Substitution - Missense(1)	p.Q125E(1)	kidney(1)																																																0							g.chr15:102292783_102292786delCTCA	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102292783_102292786delCTCA														0	829_832	+									RNA	DEL	ENST00000561463.1	37																																																																																						0.603	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		7	293						7	293	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29113498	29113498	+	RNA	DEL	T	T	-	rs11366120	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:29113498delT	ENST00000562618.1	-	0	1840				RRN3P2_ENST00000564580.1_RNA																							AGGAGGTGGAttttttttttc	0.542													|||unknown(NO_COVERAGE)	2145	0.428315	0.5507	0.4856	5008	,	,		13214	0.248		0.4334	False		,,,				2504	0.4029					ENST00000564580.1																			0																																																			0							g.chr16:29113498delT																													16.37:g.29113498delT														0	1360	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.542	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			11	196						11	196	---	---	---	---
RP11-44F14.1	0	broad.mit.edu	37	16	53404542	53404543	+	RNA	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:53404542_53404543insA	ENST00000565421.1	-	0	410																											TCTCCTTTCTCAAACTTAACCT	0.327																																						ENST00000565421.1																			0																																																			0							g.chr16:53404542_53404543insA																													16.37:g.53404545_53404545dupA														0	410	-									RNA	INS	ENST00000565421.1	37																																																																																						0.327	RP11-44F14.1-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000422364.2			17	236						17	236	---	---	---	---
MT1A	4489	broad.mit.edu	37	16	56670304	56670306	+	5'Flank	DEL	CTT	CTT	-	rs527712973	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:56670304_56670306delCTT	ENST00000290705.8	+	0	0				MT1JP_ENST00000564564.1_RNA	NM_005946.2	NP_005937.2	P04731	MT1A_HUMAN	metallothionein 1A						cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)	3					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTGCTGTACCTTCTTCATCTCA	0.581														9	0.00179712	0.0	0.0	5008	,	,		21738	0.0		0.003	False		,,,				2504	0.0061					ENST00000564564.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr16:56670304_56670306delCTT	BC029475	CCDS32454.1	16q13	2012-10-02	2007-03-02			ENSG00000205362		"""Metallothioneins"""	7393	protein-coding gene	gene with protein product		156350	"""metallothionein 1S"""	MT1, MT1S		6089206, 6327055	Standard	NM_005946		Approved		uc002ejq.3	P04731			16.37:g.56670307_56670309delCTT	Exception_encountered													0	630_632	+								Q86YX5	RNA	DEL	ENST00000290705.8	37		CCDS32454.1																																																																																				0.581	MT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434324.1	NM_005946		8	311						8	311	---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67763279	67763281	+	In_Frame_Del	DEL	GAG	GAG	-	rs141826437	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:67763279_67763281delGAG	ENST00000317506.3	-	10	1369_1371	c.1254_1256delCTC	c.(1252-1257)tcctcg>tcg	p.418_419SS>S	RANBP10_ENST00000536251.1_In_Frame_Del_p.189_190SS>S|RANBP10_ENST00000602677.1_In_Frame_Del_p.418_419SS>S|RANBP10_ENST00000448631.2_In_Frame_Del_p.362_363SS>S|RANBP10_ENST00000411657.2_In_Frame_Del_p.301_302SS>S	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	418	Ser-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.S418S(2)		endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		ggaagaggacgaggaggaggagg	0.567																																						ENST00000317506.3																			2	Substitution - coding silent(2)	p.S418S(2)	endometrium(2)	endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23						c.(1252-1257)tcg>tc		RAN binding protein 10																																				SO:0001651	inframe_deletion	57610							g.chr16:67763279_67763281delGAG	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.1254_1256delCTC	16.37:g.67763288_67763290delGAG	ENSP00000316589:p.Ser422del					RANBP10_ENST00000536251.1_In_Frame_Del_p.SS191del|RANBP10_ENST00000602677.1_In_Frame_Del_p.SS420del|RANBP10_ENST00000448631.2_In_Frame_Del_p.SS364del|RANBP10_ENST00000411657.2_In_Frame_Del_p.SS303del	p.SS420del	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)	10	1369_1371	-		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)	420			Ser-rich.		A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	In_Frame_Del	DEL	ENST00000317506.3	37	c.1254_1256delCTC	CCDS32469.1																																																																																				0.567	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		9	258						9	258	---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89613072	89613073	+	Frame_Shift_Ins	INS	-	-	G	rs111475461	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr16:89613072_89613073insG	ENST00000268704.2	+	11	1471_1472	c.1456_1457insG	c.(1456-1458)cggfs	p.R486fs		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	486			R -> Q (in dbSNP:rs111475461).		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GCAGGAGAGGCGGGAGATTTTT	0.594																																						ENST00000268704.2																			0				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20						c.(1456-1458)ggafs		spastic paraplegia 7 (pure and complicated autosomal recessive)																																				SO:0001589	frameshift_variant	6687				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding	g.chr16:89613072_89613073insG	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1459dupG	16.37:g.89613075_89613075dupG	ENSP00000268704:p.Arg486fs						p.G486fs	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)	11	1471_1472	+		all_hematologic(23;0.00824)|Colorectal(91;0.102)	486		R -> Q.			O75756|Q2TB70|Q58F00|Q96IB0	Frame_Shift_Ins	INS	ENST00000268704.2	37	c.1456_1457insG	CCDS10977.1																																																																																				0.594	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		14	840						14	840	---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8415820	8415822	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:8415820_8415822delTTC	ENST00000269243.4	-	22	2944_2946	c.2806_2808delGAA	c.(2806-2808)gaadel	p.E936del	MYH10_ENST00000360416.3_In_Frame_Del_p.E967del|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000396239.1_In_Frame_Del_p.E957del|MYH10_ENST00000379980.4_In_Frame_Del_p.E952del	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	936					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TTTGGTTTCTTTCTTCTTCTTCT	0.35																																						ENST00000360416.3																			0				breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						c.(2899-2901)del		myosin, heavy chain 10, non-muscle																																				SO:0001651	inframe_deletion	4628				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity	g.chr17:8415820_8415822delTTC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2806_2808delGAA	17.37:g.8415829_8415831delTTC	ENSP00000269243:p.Glu936del					MYH10_ENST00000269243.4_In_Frame_Del_p.E936del|MYH10_ENST00000396239.1_In_Frame_Del_p.E957del|MYH10_ENST00000379980.4_In_Frame_Del_p.E952del	p.E967del	NM_001256012.1	NP_001242941.1	P35580	MYH10_HUMAN			24	3037_3039	-			936					B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	In_Frame_Del	DEL	ENST00000269243.4	37	c.2899_2901delGAA	CCDS11144.1																																																																																				0.350	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			8	307						8	307	---	---	---	---
AC005863.1	0	broad.mit.edu	37	17	14673542	14673543	+	lincRNA	INS	-	-	T			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:14673542_14673543insT	ENST00000379640.1	-	0	354_355																											GCTGGTCCCAGTTTTTTTTTCT	0.45																																						ENST00000379640.1																			0																	4,4260		0,4,2128						0.2	0.0			65	15,8239		0,15,4112	no	intergenic				0,19,6240	A1A1,A1R,RR		0.1817,0.0938,0.1518				19,12499						0							g.chr17:14673542_14673543insT																													17.37:g.14673551_14673551dupT														0	354_355	-									RNA	INS	ENST00000379640.1	37																																																																																						0.450	AC005863.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000130001.1			9	235						9	235	---	---	---	---
SNORD3C	780853	broad.mit.edu	37	17	19091512	19091517	+	lincRNA	DEL	GGGAGT	GGGAGT	-	rs556489629	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:19091512_19091517delGGGAGT	ENST00000362428.1	-	0	432				SNORD3A_ENST00000365494.1_lincRNA					small nucleolar RNA, C/D box 3C																		ctccgtattggggagtgagagggaga	0.539																																						ENST00000365494.1																			0																	27,1275		5,17,629						-0.1	0.0			5	198,1962		25,148,907	no	intergenic				30,165,1536	A1A1,A1R,RR		9.1667,2.0737,6.4991				225,3237						0							g.chr17:19091512_19091517delGGGAGT			17p11.2	2013-09-05			ENSG00000199298	ENSG00000264940			33191	non-coding RNA	RNA, small nucleolar						9365252	Standard	NR_006881		Approved	U3-3					17.37:g.19091512_19091517delGGGAGT														0	184_189	+									RNA	DEL	ENST00000362428.1	37																																																																																						0.539	SNORD3C-201	KNOWN	basic	snoRNA	lincRNA		NR_006881		13	1151						13	1151	---	---	---	---
RP11-178C3.1	0	broad.mit.edu	37	17	58050857	58050857	+	IGR	DEL	G	G	-	rs375748922		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:58050857delG	ENST00000591035.1	+	0	481				RP11-178C3.2_ENST00000586209.1_lincRNA																							TTTTTTTTTTGGCAGTTTTTA	0.423																																						ENST00000586209.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr17:58050857delG																													17.37:g.58050857delG														0	158	+									RNA	DEL	ENST00000591035.1	37																																																																																						0.423	RP11-178C3.1-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000449157.1			9	112						9	112	---	---	---	---
LRRC37A16P	651250	broad.mit.edu	37	17	66141017	66141017	+	RNA	DEL	C	C	-	rs376314569|rs368840037		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:66141017delC	ENST00000590019.1	-	0	70									leucine rich repeat containing 37, member A16, pseudogene																		AAGATTTCTACAAAAAAAAAA	0.323																																						ENST00000590019.1																			0																																																			0							g.chr17:66141017delC			17q24.2	2012-10-18				ENSG00000267023			43820	pseudogene	pseudogene							Standard	NG_023507		Approved				OTTHUMG00000180160		17.37:g.66141017delC														0	70	-									RNA	DEL	ENST00000590019.1	37																																																																																						0.323	LRRC37A16P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000450078.1			8	271						8	271	---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78354713	78354713	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:78354713delC	ENST00000582970.1	+	56	13866	c.13723delC	c.(13723-13725)cccfs	p.P4576fs	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Frame_Shift_Del_p.P2649fs|RNF213_ENST00000508628.2_Frame_Shift_Del_p.P4625fs|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4576					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCGAGGGCTGCCCCCAGTGGT	0.587																																						ENST00000582970.1																			0				NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130						c.(13723-13725)ccfs		ring finger protein 213							205.0	214.0	211.0					17																	78354713		2203	4300	6503	SO:0001589	frameshift_variant	57674							g.chr17:78354713delC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13723delC	17.37:g.78354713delC	ENSP00000464087:p.Pro4576fs					CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Frame_Shift_Del_p.P4625fs|RNF213_ENST00000336301.6_Frame_Shift_Del_p.P2649fs	p.P4576fs	NM_001256071.1	NP_001243000.1	Q9HCF4	ALO17_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)		56	13866	+	all_neural(118;0.0538)		0					C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Frame_Shift_Del	DEL	ENST00000582970.1	37	c.13723delC	CCDS58606.1																																																																																				0.587	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		7	2081						7	2081	---	---	---	---
SLC25A10	1468	broad.mit.edu	37	17	79686865	79686865	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr17:79686865delT	ENST00000350690.5	+	10	796	c.710delT	c.(709-711)gttfs	p.V237fs	SLC25A10_ENST00000541223.1_Frame_Shift_Del_p.V392fs|SLC25A10_ENST00000545862.1_Frame_Shift_Del_p.V194fs|SLC25A10_ENST00000571730.1_Frame_Shift_Del_p.V392fs|SLC25A10_ENST00000331531.5_Frame_Shift_Del_p.V246fs	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	237					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	CTGCAGGGCGTTTTCCACTGC	0.617																																						ENST00000331531.5																			0				endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14						c.(736-738)gtfs		solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	Succinic acid(DB00139)						176.0	203.0	194.0					17																	79686865		2203	4300	6503	SO:0001589	frameshift_variant	1468				gluconeogenesis|mitochondrial transport	integral to membrane|mitochondrial inner membrane|nucleus	protein binding	g.chr17:79686865delT		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.710delT	17.37:g.79686865delT	ENSP00000345580:p.Val237fs					SLC25A10_ENST00000350690.5_Frame_Shift_Del_p.V237fs|SLC25A10_ENST00000541223.1_Frame_Shift_Del_p.V392fs|SLC25A10_ENST00000545862.1_Frame_Shift_Del_p.V194fs|SLC25A10_ENST00000571730.1_Frame_Shift_Del_p.V392fs	p.V246fs	NM_001270888.1	NP_001257817.1	Q9UBX3	DIC_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		10	857	+	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		237					Q542Z3|Q96BA1|Q96IP1	Frame_Shift_Del	DEL	ENST00000350690.5	37	c.737delT	CCDS11786.1																																																																																				0.617	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1			7	2209						7	2209	---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20572852	20572853	+	Frame_Shift_Ins	INS	-	-	A	rs200956310		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr18:20572852_20572853insA	ENST00000399722.2	+	11	1413_1414	c.1062_1063insA	c.(1063-1065)aaafs	p.K355fs	RBBP8_ENST00000360790.5_Frame_Shift_Ins_p.K355fs|RBBP8_ENST00000399725.2_Frame_Shift_Ins_p.K355fs|RBBP8_ENST00000327155.5_Frame_Shift_Ins_p.K355fs	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	355					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.K357fs*3(2)|p.K355E(2)|p.G354G(2)		central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			TACAGCCTGGGAAAAAAAAACA	0.361								Homologous recombination																														ENST00000399722.2																			6	Substitution - Missense(2)|Deletion - Frameshift(2)|Substitution - coding silent(2)	p.K357fs*3(2)|p.K355E(2)|p.G354G(2)	ovary(2)|central_nervous_system(2)|endometrium(2)	central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24						c.(1060-1065)ggaaaafs	Homologous recombination	retinoblastoma binding protein 8																																				SO:0001589	frameshift_variant	5932				cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity	g.chr18:20572852_20572853insA	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1071dupA	18.37:g.20572861_20572861dupA	ENSP00000382628:p.Lys355fs					RBBP8_ENST00000360790.5_Frame_Shift_Ins_p.GK354fs|RBBP8_ENST00000327155.5_Frame_Shift_Ins_p.GK354fs|RBBP8_ENST00000399725.2_Frame_Shift_Ins_p.GK354fs	p.GK354fs	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	OV - Ovarian serous cystadenocarcinoma(1;0.00196)		11	1413_1414	+	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		354					A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Frame_Shift_Ins	INS	ENST00000399722.2	37	c.1062_1063insA	CCDS11875.1																																																																																				0.361	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		13	487						13	487	---	---	---	---
CCDC178	374864	broad.mit.edu	37	18	30913143	30913143	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr18:30913143delT	ENST00000383096.3	-	10	1056	c.874delA	c.(874-876)atgfs	p.M292fs	CCDC178_ENST00000583930.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000406524.2_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000300227.8_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000402325.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000403303.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579947.1_Frame_Shift_Del_p.M292fs			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	292								p.M292fs*3(2)									TTTACCTCCATTTTTTTTTTA	0.318																																						ENST00000383096.3																			2	Deletion - Frameshift(2)	p.M292fs*3(2)	lung(2)								c.(874-876)tgfs		coiled-coil domain containing 178			,	7,25,4232		0,0,7,1,23,2101	83.0	81.0	82.0		,	-10.6	0.0	18		83	4,25,8225		0,0,4,1,23,4099	no	codingComplex,codingComplex	C18orf34	NM_198995.2,NM_001105528.1	,	0,0,11,2,46,6200	A1A1,A1A2,A1R,A2A2,A2R,RR		0.3513,0.7505,0.4873	,	,	30913143	11,50,12457	2203	4300	6503	SO:0001589	frameshift_variant	374864							g.chr18:30913143delT	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.874delA	18.37:g.30913143delT	ENSP00000372576:p.Met292fs					CCDC178_ENST00000402325.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000403303.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000583930.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000406524.2_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579947.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000300227.8_Frame_Shift_Del_p.M292fs	p.M292fs							10	1056	-								A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Frame_Shift_Del	DEL	ENST00000383096.3	37	c.874delA	CCDS42424.1																																																																																				0.318	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		10	215						10	215	---	---	---	---
LMAN1	3998	broad.mit.edu	37	18	57013193	57013194	+	Frame_Shift_Ins	INS	-	-	T	rs553350987		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr18:57013193_57013194insT	ENST00000251047.5	-	8	1629_1630	c.912_913insA	c.(910-915)aaagagfs	p.E305fs	LMAN1_ENST00000587940.1_5'Flank	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	305					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TGGAATTCCTCTTTTTTTTTAT	0.455																																						ENST00000251047.5																			0				breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	GRCh37	CI992039	LMAN1	I		c.(910-915)aaaggafs		lectin, mannose-binding, 1	Antihemophilic Factor(DB00025)			1,4263		0,1,2131						5.7	1.0			139	0,8254		0,0,4127	no	frameshift	LMAN1	NM_005570.3		0,1,6258	A1A1,A1R,RR		0.0,0.0235,0.0080				1,12517				SO:0001589	frameshift_variant	3998				blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding	g.chr18:57013193_57013194insT	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.913dupA	18.37:g.57013202_57013202dupT	ENSP00000251047:p.Glu305fs						p.G305fs	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN			8	1629_1630	-		Colorectal(73;0.0946)	305					Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Frame_Shift_Ins	INS	ENST00000251047.5	37	c.912_913insA	CCDS11974.1																																																																																				0.455	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		10	601						10	601	---	---	---	---
CYP4F3	4051	broad.mit.edu	37	19	15769322	15769322	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:15769322delT	ENST00000221307.8	+	11	1318	c.1271delT	c.(1270-1272)gttfs	p.V424fs	CYP4F3_ENST00000585846.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000591058.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000586182.2_Frame_Shift_Del_p.V424fs	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	424					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						CTCATCAGTGTTTTTGGAACC	0.622																																						ENST00000221307.7																			0				endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						c.(1270-1272)gtfs		cytochrome P450, family 4, subfamily F, polypeptide 3							139.0	148.0	145.0					19																	15769322		2203	4300	6503	SO:0001589	frameshift_variant	4051				leukotriene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding	g.chr19:15769322delT	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.1271delT	19.37:g.15769322delT	ENSP00000221307:p.Val424fs					CYP4F3_ENST00000591058.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000586182.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000585846.1_Frame_Shift_Del_p.V424fs	p.V424fs	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN			11	1319	+			424					B7Z8Z3|O60634|Q5U740	Frame_Shift_Del	DEL	ENST00000221307.8	37	c.1271delT	CCDS12332.1																																																																																				0.622	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		7	1620						7	1620	---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	22002025	22002026	+	Splice_Site	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:22002025_22002026insA	ENST00000354959.4	-	2	173		c.e2-2		ZNF43_ENST00000595461.1_Splice_Site|ZNF43_ENST00000598288.1_Splice_Site|ZNF43_ENST00000598381.1_Splice_Site|ZNF43_ENST00000594012.1_Splice_Site	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		CAATGGTCCCTAAAAAAAACAA	0.386																																						ENST00000594012.1																			1	Unknown(1)	p.?(1)	ovary(1)	autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51						c.e5-2		zinc finger protein 43																																				SO:0001630	splice_region_variant	7594				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:22002025_22002026insA	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.4-2->T	19.37:g.22002033_22002033dupA						ZNF43_ENST00000598288.1_Splice_Site|ZNF43_ENST00000598381.1_Splice_Site|ZNF43_ENST00000354959.4_Splice_Site|ZNF43_ENST00000595461.1_Splice_Site		NM_001256649.1|NM_001256651.1|NM_001256653.1|NM_001256654.1	NP_001243578.1|NP_001243580.1|NP_001243582.1|NP_001243583.1	P17038	ZNF43_HUMAN		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)	5	500	-		Renal(1328;0.000219)|Hepatocellular(1079;0.121)						A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Splice_Site	INS	ENST00000354959.4	37		CCDS12413.2																																																																																				0.386	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	Intron	8	938						8	938	---	---	---	---
HAUS5	23354	broad.mit.edu	37	19	36108990	36108990	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:36108990delC	ENST00000203166.5	+	10	739	c.714delC	c.(712-714)cacfs	p.H238fs	HAUS5_ENST00000379045.2_Frame_Shift_Del_p.H238fs	NM_015302.1	NP_056117.1	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	238					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				NS(1)|breast(2)|cervix(3)|endometrium(1)|large_intestine(2)|lung(5)|skin(2)	16						TGACAAACCACCCCCCAGGCC	0.642																																						ENST00000203166.5																			0				NS(1)|breast(2)|cervix(3)|endometrium(1)|large_intestine(2)|lung(5)|skin(2)	16						c.(712-714)cafs		HAUS augmin-like complex, subunit 5							80.0	89.0	86.0					19																	36108990		2078	4212	6290	SO:0001589	frameshift_variant	23354				cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle		g.chr19:36108990delC	AB020648	CCDS42550.1	19q13.12	2012-02-22	2009-04-20	2009-04-20	ENSG00000249115	ENSG00000249115		"""HAUS augmin-like complex subunits"""	29130	protein-coding gene	gene with protein product		613432	"""KIAA0841"""	KIAA0841		10048485, 19427217	Standard	NM_015302		Approved	dgt5	uc002oam.1	O94927	OTTHUMG00000048110	ENST00000203166.5:c.714delC	19.37:g.36108990delC	ENSP00000439056:p.His238fs					HAUS5_ENST00000379045.2_Frame_Shift_Del_p.H238fs	p.H238fs	NM_015302.1	NP_056117.1	O94927	HAUS5_HUMAN			10	739	+			238					B2RXK1|Q6P2P7|Q7L3D5|Q96CT8	Frame_Shift_Del	DEL	ENST00000203166.5	37	c.714delC	CCDS42550.1																																																																																				0.642	HAUS5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459055.2			7	1081						7	1081	---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36583666	36583668	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:36583666_36583668delGCA	ENST00000270301.7	+	19	2286_2288	c.2286_2288delGCA	c.(2284-2289)cggcag>cgg	p.Q766del	WDR62_ENST00000401500.2_In_Frame_Del_p.Q766del			O43379	WDR62_HUMAN	WD repeat domain 62	766					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TTGACCACCGGCAGCAGCAGCAG	0.616																																						ENST00000401500.2																			0				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43						c.(2284-2289)cgg>cg		WD repeat domain 62																																				SO:0001651	inframe_deletion	284403				cerebral cortex development	nucleus		g.chr19:36583666_36583668delGCA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2286_2288delGCA	19.37:g.36583675_36583677delGCA	ENSP00000270301:p.Gln766del					WDR62_ENST00000270301.7_In_Frame_Del_p.RQ762del	p.RQ762del	NM_001083961.1|NM_173636.4	NP_001077430.1|NP_775907.4	O43379	WDR62_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.06)		19	2321_2323	+	Esophageal squamous(110;0.162)		762					Q63HP9|Q659D7|Q8NBF7|Q96AD9	In_Frame_Del	DEL	ENST00000270301.7	37	c.2286_2288delGCA	CCDS33001.1																																																																																				0.616	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		7	889						7	889	---	---	---	---
LYPD3	27076	broad.mit.edu	37	19	43969653	43969655	+	In_Frame_Del	DEL	AGC	AGC	-	rs141441894	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:43969653_43969655delAGC	ENST00000244333.3	-	1	157_159	c.69_71delGCT	c.(67-72)ctgctt>ctt	p.23_24LL>L		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	23					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				ACCTCCGCGAAGCAGCAGCAGCA	0.675																																						ENST00000244333.3																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11						c.(67-72)ctt>ct		LY6/PLAUR domain containing 3																																				SO:0001651	inframe_deletion	27076					anchored to plasma membrane		g.chr19:43969653_43969655delAGC	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.69_71delGCT	19.37:g.43969662_43969664delAGC	ENSP00000244333:p.Leu24del						p.LL23del	NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN			1	157_159	-		Prostate(69;0.0153)	23					Q9UJ74	In_Frame_Del	DEL	ENST00000244333.3	37	c.69_71delGCT	CCDS12620.1																																																																																				0.675	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		9	843						9	843	---	---	---	---
PNMAL1	55228	broad.mit.edu	37	19	46973195	46973197	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:46973195_46973197delCTT	ENST00000313683.10	-	2	1401_1403	c.1096_1098delAAG	c.(1096-1098)aagdel	p.K366del	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Splice_Site_p.K366del	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	366										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CCAAGCTCACCTTCTTCTTCTTC	0.562																																						ENST00000313683.10																			0				cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						c.(1096-1098)del		paraneoplastic Ma antigen family-like 1																																				SO:0001651	inframe_deletion	55228							g.chr19:46973195_46973197delCTT	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.1096_1098delAAG	19.37:g.46973204_46973206delCTT	ENSP00000318131:p.Lys366del					PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Splice_Site_p.K366_splice	p.K366del	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)	2	1401_1403	-		Ovarian(192;0.00965)|all_neural(266;0.0459)	366					A8K2F3|Q5U638|Q8N3H4|Q9NVE8	In_Frame_Del	DEL	ENST00000313683.10	37	c.1096_1098delAAG	CCDS33059.1																																																																																				0.562	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		8	1193						8	1193	---	---	---	---
MAMSTR	284358	broad.mit.edu	37	19	49218105	49218106	+	Frame_Shift_Ins	INS	-	-	G	rs373516785		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:49218105_49218106insG	ENST00000318083.6	-	6	548_549	c.485_486insC	c.(484-486)ccafs	p.P162fs	MAMSTR_ENST00000419611.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000594582.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000377367.3_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000356751.4_Frame_Shift_Ins_p.P59fs			Q6ZN01	MASTR_HUMAN	MEF2 activating motif and SAP domain containing transcriptional regulator	162	Pro-rich.				positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(1)|ovary(1)	2						CCAACTTGTGTGGGGGGGGCGA	0.569																																						ENST00000318083.6																			0				endometrium(1)|ovary(1)	2						c.(484-486)ccafs		MEF2 activating motif and SAP domain containing transcriptional regulator																																				SO:0001589	frameshift_variant	284358				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding	g.chr19:49218105_49218106insG	AK093389	CCDS12730.1, CCDS46137.1, CCDS74415.1	19q13.33	2009-07-09			ENSG00000176909	ENSG00000176909			26689	protein-coding gene	gene with protein product	"""MEF2-activating SAP transcriptional regulator"""	610349				16818234	Standard	NM_182574		Approved	MASTR, FLJ36070	uc002pkg.2	Q6ZN01		ENST00000318083.6:c.486dupC	19.37:g.49218113_49218113dupG	ENSP00000324175:p.Pro162fs					MAMSTR_ENST00000377367.3_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000419611.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000594582.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000356751.4_Frame_Shift_Ins_p.P59fs	p.P162fs			Q6ZN01	MASTR_HUMAN			6	548_549	-			162			Pro-rich.		B7ZKX4|Q3KQU9|Q8N9Y3	Frame_Shift_Ins	INS	ENST00000318083.6	37	c.485_486insC	CCDS46137.1																																																																																				0.569	MAMSTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466179.1	NM_182574		8	580						8	580	---	---	---	---
LILRA4	23547	broad.mit.edu	37	19	54843564	54843565	+	IGR	INS	-	-	C	rs556721604|rs535654307|rs35566239|rs5828583	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:54843564_54843565insC	ENST00000291759.4	-	0	1944				AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4						immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGGCTGCTCCTCCCCAGGCTGC	0.723													?|CCCC|CCCCC|unsure	2000	0.399361	0.1437	0.3905	5008	,	,		12788	0.5903		0.4394	False		,,,				2504	0.5133					ENST00000507363.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr19:54843564_54843565insC	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355		19.37:g.54843568_54843568dupC														0	430	-								Q32MC4	RNA	INS	ENST00000291759.4	37		CCDS12890.1																																																																																				0.723	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		10	16						10	16	---	---	---	---
ZNF134	7693	broad.mit.edu	37	19	58132432	58132432	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr19:58132432delT	ENST00000396161.5	+	3	1255	c.945delT	c.(943-945)cctfs	p.P315fs		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		GAGAAAATCCTTATGATTGCA	0.413																																						ENST00000396161.5																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11						c.(943-945)ccfs		zinc finger protein 134							133.0	136.0	135.0					19																	58132432		2201	4300	6501	SO:0001589	frameshift_variant	7693					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:58132432delT	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.945delT	19.37:g.58132432delT	ENSP00000379464:p.Pro315fs						p.P315fs	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)	3	1255	+		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)	315					Q9Y4B2	Frame_Shift_Del	DEL	ENST00000396161.5	37	c.945delT	CCDS42638.1																																																																																				0.413	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		44	1060						44	1060	---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29625899	29625900	+	Frame_Shift_Ins	INS	-	-	AT	rs201509828		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:29625899_29625900insAT	ENST00000278882.3	+	5	523_524	c.143_144insAT	c.(142-147)aaatatfs	p.KY48fs	FRG1B_ENST00000358464.4_Frame_Shift_Ins_p.KY48fs|FRG1B_ENST00000439954.2_Frame_Shift_Ins_p.KY53fs			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	48										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGCTATGGAAAATATCTTGGTA	0.342																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(142-144)atafs																																						SO:0001589	frameshift_variant	0							g.chr20:29625899_29625900insAT			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.146_147dupAT	20.37:g.29625902_29625903dupAT	ENSP00000278882:p.Lys48fs					FRG1B_ENST00000358464.4_Frame_Shift_Ins_p.I48fs|FRG1B_ENST00000439954.2_Frame_Shift_Ins_p.I53fs	p.I48fs							5	523_524	+								C4AME5	Frame_Shift_Ins	INS	ENST00000278882.3	37	c.143_144insAT																																																																																					0.342	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		28	691						28	691	---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39977799	39977799	+	Frame_Shift_Del	DEL	C	C	-	rs559175371	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:39977799delC	ENST00000373257.3	+	5	716	c.625delC	c.(625-627)cccfs	p.P210fs		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	210					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				TGGCGAGTGGCCCCCCCAGGC	0.537													CCCCCCC|CCCCCCC|CCCCCC|deletion	3	0.000599042	0.0	0.0	5008	,	,		17869	0.0		0.003	False		,,,				2504	0.0					ENST00000373257.3																			0				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						c.(625-627)ccfs		lipin 3				6,0,4258		0,0,6,0,0,2126	70.0	71.0	71.0			-1.4	0.0	20		72	6,2,8246		0,0,6,0,2,4119	no	codingComplex	LPIN3	NM_022896.1		0,0,12,0,2,6245	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0969,0.1407,0.1118			39977799	12,2,12504	2203	4300	6503	SO:0001589	frameshift_variant	64900				fatty acid metabolic process	nucleus	phosphatidate phosphatase activity	g.chr20:39977799delC	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.625delC	20.37:g.39977799delC	ENSP00000362354:p.Pro210fs						p.P210fs	NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN			5	716	+		Myeloproliferative disorder(115;0.000739)	210					B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Frame_Shift_Del	DEL	ENST00000373257.3	37	c.625delC	CCDS33469.1																																																																																				0.537	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		7	634						7	634	---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52557949	52557950	+	IGR	INS	-	-	TT	rs72548465|rs201903487|rs141488543|rs2870294		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:52557949_52557950insTT	ENST00000395961.3	-	0	3303				AC005220.3_ENST00000450473.1_RNA	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			gtgtgtgtgtgtgtgtgtgcgc	0.5																																						ENST00000450473.1																			0																	194,519,1821		59,6,70,144,225,763						1.3	0.0		dbSNP_101	4	657,726,3403		150,19,338,195,317,1374	no	intergenic				209,25,408,339,542,2137	A1A1,A1A2,A1R,A2A2,A2R,RR		28.8968,28.1373,28.6339				851,1245,5224				SO:0001628	intergenic_variant	0							g.chr20:52557949_52557950insTT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772		20.37:g.52557949_52557950insTT														0	550	+								A0AVG5|Q68CZ3	RNA	INS	ENST00000395961.3	37		CCDS13444.1																																																																																				0.500	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		6	11						6	11	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61512380	61512381	+	Frame_Shift_Ins	INS	-	-	G			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr20:61512380_61512381insG	ENST00000266070.4	-	16	5252_5253	c.4927_4928insC	c.(4927-4929)cgcfs	p.R1643fs	DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.R1643fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1643					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CGTGGCGGGGCGGGTGCCCTCC	0.728																																					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	ENST00000266070.4																			0				NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99						c.(4927-4929)cccfs		death inducer-obliterator 1																																				SO:0001589	frameshift_variant	11083				apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding	g.chr20:61512380_61512381insG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.4928dupC	20.37:g.61512383_61512383dupG	ENSP00000266070:p.Arg1643fs					DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.P1643fs	p.P1643fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN			16	5252_5253	-	Breast(26;5.68e-08)		1643					A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Frame_Shift_Ins	INS	ENST00000266070.4	37	c.4927_4928insC	CCDS33506.1																																																																																				0.728	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		10	139						10	139	---	---	---	---
ANKRD20A11P	391267	broad.mit.edu	37	21	15343608	15343609	+	RNA	INS	-	-	A			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr21:15343608_15343609insA	ENST00000344693.5	-	0	736				RNU6-954P_ENST00000411355.1_RNA	NR_027270.1				ankyrin repeat domain 20 family, member A11, pseudogene																		TAAAACAGCAGAAAAAATTAAT	0.272																																						ENST00000344693.5																			0																																																			0							g.chr21:15343608_15343609insA			21q11.2	2011-11-23			ENSG00000215559	ENSG00000215559			42024	pseudogene	pseudogene			"""chromosome 21 open reading frame 81"""	C21orf81			Standard	NR_027270		Approved		uc002yjj.4		OTTHUMG00000074237		21.37:g.15343614_15343614dupA								NR_027270.1						0	736	-									RNA	INS	ENST00000344693.5	37																																																																																						0.272	ANKRD20A11P-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157750.1			15	507						15	507	---	---	---	---
ADAMTS5	11096	broad.mit.edu	37	21	28296615	28296615	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr21:28296615delA	ENST00000284987.5	-	8	2671	c.2550delT	c.(2548-2550)tttfs	p.F850fs	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	850	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TCTTGGGAACAAAAAAGCTAT	0.478																																					Esophageal Squamous(53;683 1080 10100 14424 45938)	ENST00000284987.5																			0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						c.(2548-2550)ttfs		ADAM metallopeptidase with thrombospondin type 1 motif, 5							114.0	119.0	117.0					21																	28296615		2203	4300	6503	SO:0001589	frameshift_variant	11096				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding	g.chr21:28296615delA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2550delT	21.37:g.28296615delA	ENSP00000284987:p.Phe850fs					AP001601.2_ENST00000426771.1_RNA	p.F850fs	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN			8	2671	-			850			Spacer.		Q52LV4|Q9UKP2	Frame_Shift_Del	DEL	ENST00000284987.5	37	c.2550delT	CCDS13579.1																																																																																				0.478	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			7	745						7	745	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20918817	20918819	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:20918817_20918819delCAG	ENST00000263205.7	+	6	601_603	c.532_534delCAG	c.(532-534)cagdel	p.Q188del	MED15_ENST00000406969.1_In_Frame_Del_p.Q162del|MED15_ENST00000542773.1_5'UTR|MED15_ENST00000292733.7_In_Frame_Del_p.Q188del|MED15_ENST00000541476.1_In_Frame_Del_p.Q162del|MED15_ENST00000425759.2_In_Frame_Del_p.Q77del|MED15_ENST00000382974.2_In_Frame_Del_p.Q117del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	188	Poly-Gln.				gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			ggcggcgctacagcagcagcagc	0.626											OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000263205.7																			0				central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25						c.(532-534)del		mediator complex subunit 15																																				SO:0001651	inframe_deletion	51586				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding	g.chr22:20918817_20918819delCAG	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.532_534delCAG	22.37:g.20918826_20918828delCAG	ENSP00000263205:p.Gln188del		OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	744	MED15_ENST00000292733.7_In_Frame_Del_p.Q188del|MED15_ENST00000425759.2_In_Frame_Del_p.Q77del|MED15_ENST00000406969.1_In_Frame_Del_p.Q162del|MED15_ENST00000542773.1_5'UTR|MED15_ENST00000541476.1_In_Frame_Del_p.Q162del|MED15_ENST00000382974.2_In_Frame_Del_p.Q117del	p.Q188del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)		6	601_603	+	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	188			Poly-Gln.		D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Del	DEL	ENST00000263205.7	37	c.532_534delCAG	CCDS33602.1																																																																																				0.626	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		8	187						8	187	---	---	---	---
IGLV4-60	28785	broad.mit.edu	37	22	22516884	22516884	+	RNA	DEL	C	C	-	rs34221567	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:22516884delC	ENST00000390284.2	+	0	172									immunoglobulin lambda variable 4-60																		CGCATGGCATCAGCAGCAGCC	0.567													C|C|-|deletion	905	0.180711	0.1074	0.2406	5008	,	,		20423	0.0575		0.4195	False		,,,				2504	0.1186					ENST00000390284.2																			0																	613,3457		73,467,1495	70.0	58.0	62.0			-5.7	0.0	22	dbSNP_126	82	3051,5071		628,1795,1638	no	intergenic				701,2262,3133	A1A1,A1R,RR		37.5646,15.0614,30.0525			22516884	3664,8528	2043	3697	5740			0							g.chr22:22516884delC	Z73667		22q11.2	2012-02-08			ENSG00000211639	ENSG00000211639		"""Immunoglobulins / IGL locus"""	5920	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000150851		22.37:g.22516884delC														0	172	+									RNA	DEL	ENST00000390284.2	37																																																																																						0.567	IGLV4-60-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000320328.1	NG_000002		7	251						7	251	---	---	---	---
SH3BP1	23616	broad.mit.edu	37	22	38039752	38039754	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:38039752_38039754delAGG	ENST00000357436.4	+	7	888_890	c.575_577delAGG	c.(574-579)aaggag>aag	p.E197del	SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000442465.2_In_Frame_Del_p.E197del|SH3BP1_ENST00000599616.1_In_Frame_Del_p.E133del|SH3BP1_ENST00000336738.5_In_Frame_Del_p.E197del|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	197	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					GAGACGCTGAAGGAGGAGGAGGA	0.606											OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000599616.1																			0				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						c.(382-387)aag>a		SH3-domain binding protein 1				1,4261		0,1,2130						5.1	1.0			112	1,8253		0,1,4126	no	coding	SH3BP1	NM_018957.3		0,2,6256	A1A1,A1R,RR		0.0121,0.0235,0.016				2,12514				SO:0001651	inframe_deletion	23616				signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding	g.chr22:38039752_38039754delAGG		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.575_577delAGG	22.37:g.38039761_38039763delAGG	ENSP00000350018:p.Glu197del		OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	875	SH3BP1_ENST00000442465.2_In_Frame_Del_p.KE192del|SH3BP1_ENST00000336738.5_In_Frame_Del_p.KE192del|SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000357436.4_In_Frame_Del_p.KE192del|Z83844.1_ENST00000456099.1_RNA	p.KE128del			Q9Y3L3	3BP1_HUMAN			5	383_385	+	Melanoma(58;0.0574)		192			BAR.		Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	In_Frame_Del	DEL	ENST00000357436.4	37	c.383_385delAGG	CCDS13952.2																																																																																				0.606	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		7	560						7	560	---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42898665	42898666	+	RNA	INS	-	-	C	rs375411583	byFrequency	TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:42898665_42898666insC	ENST00000359906.2	+	0	409					NR_027786.1		Q9NQF3	SERHL_HUMAN	serine hydrolase-like								hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)	2						CCCATATGGTGCCCCCCCCCCA	0.589																																						ENST00000359906.2																			0				endometrium(1)|large_intestine(1)	2								serine hydrolase-like																																						94009							g.chr22:42898665_42898666insC	AL365513		22q13.2-q13.31	2009-10-06				ENSG00000172250			14408	protein-coding gene	gene with protein product	"""kraken-like"""	607979				11352564	Standard	NR_027786		Approved	HS126B42, BK126B4.1, dJ222E13.1	uc021wql.1	Q9NQF3			22.37:g.42898675_42898675dupC								NR_027786.1						0	409	+								Q5JZ95|Q9UH21	RNA	INS	ENST00000359906.2	37																																																																																						0.589	SERHL-001	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000320498.2	NM_170694		7	26						7	26	---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43213780	43213780	+	Frame_Shift_Del	DEL	T	T	-	rs552164906		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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		8	878						8	878	---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45802384	45802384	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:45802384delT	ENST00000357450.4	-	4	571	c.572delA	c.(571-573)aatfs	p.N191fs	SMC1B_ENST00000404354.3_Frame_Shift_Del_p.N191fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	191					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TGCCGCTATATTTTTTTTCTT	0.343																																						ENST00000357450.4																			0				breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37						c.(571-573)atfs		structural maintenance of chromosomes 1B							80.0	76.0	78.0					22																	45802384		1813	4072	5885	SO:0001589	frameshift_variant	27127				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding	g.chr22:45802384delT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.572delA	22.37:g.45802384delT	ENSP00000350036:p.Asn191fs					SMC1B_ENST00000404354.3_Frame_Shift_Del_p.N191fs	p.N191fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)	4	571	-		Ovarian(80;0.00965)|all_neural(38;0.0416)	191					A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Frame_Shift_Del	DEL	ENST00000357450.4	37	c.572delA	CCDS43027.1																																																																																				0.343	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		8	444						8	444	---	---	---	---
MLC1	23209	broad.mit.edu	37	22	50502593	50502595	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chr22:50502593_50502595delAGC	ENST00000311597.5	-	11	1533_1535	c.927_929delGCT	c.(925-930)ctgcta>cta	p.309_310LL>L	MLC1_ENST00000450140.2_In_Frame_Del_p.257_258LL>L|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_In_Frame_Del_p.275_276LL>L|MLC1_ENST00000535444.1_In_Frame_Del_p.230_231LL>L|MLC1_ENST00000395876.2_In_Frame_Del_p.309_310LL>L|MLC1_ENST00000431262.2_In_Frame_Del_p.279_280LL>L	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	309			L -> M (in a pedigree affected by schizophrenia; dbSNP:rs80358240). {ECO:0000269|PubMed:11326298}.		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		caggagcactagcagcagcagca	0.655																																						ENST00000311597.5																			0				endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18	GRCh37	CD030152	MLC1	D		c.(925-930)cta>ct		megalencephalic leukoencephalopathy with subcortical cysts 1																																				SO:0001651	inframe_deletion	23209					basolateral plasma membrane|endosome|integral to membrane|integral to membrane of membrane fraction	ion channel activity	g.chr22:50502593_50502595delAGC	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.927_929delGCT	22.37:g.50502602_50502604delAGC	ENSP00000310375:p.Leu310del					MLC1_ENST00000538737.1_In_Frame_Del_p.LL275del|MLC1_ENST00000535444.1_In_Frame_Del_p.LL230del|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000431262.2_In_Frame_Del_p.LL279del|MLC1_ENST00000395876.2_In_Frame_Del_p.LL309del|MLC1_ENST00000450140.2_In_Frame_Del_p.LL257del	p.LL309del	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)	11	1533_1535	-		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)	309		L -> M (in a pedigree affected by schizophrenia).			B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	In_Frame_Del	DEL	ENST00000311597.5	37	c.927_929delGCT	CCDS14083.1																																																																																				0.655	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166		7	118						7	118	---	---	---	---
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Start_Codon_Del	DEL	TCCTCGAGGCAGCC	TCCTCGAGGCAGCC	-	rs78182391		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	ENST00000375992.3	-	0	139_152					NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 11						inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)	p.?(5)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.692										HNSCC(48;0.14)				2406	0.637351	0.497	0.4928	3775	,	,		5662	0.4464		0.4553	False		,,,				2504	0.5102				GBM(38;198 791 1498 11752 13599)	ENST00000375992.3																			5	Unknown(5)	p.?(5)	upper_aerodigestive_tract(2)|prostate(1)|breast(1)|central_nervous_system(1)	breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9								nudix (nucleoside diphosphate linked moiety X)-type motif 11				1710,202		758,11,183,87,17						3.0	1.0		dbSNP_131	12	3133,173		1220,1,692,66,40	no	frameshift	NUDT11	NM_018159.3		1978,12,875,153,57	A1A1,A1R,A1,RR,R		5.2329,10.5649,7.1867				4843,375				SO:0001582	initiator_codon_variant	0					cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	AK001490	CCDS43952.1	Xp11.22-p11.1	2014-05-20			ENSG00000196368	ENSG00000196368		"""Nudix motif containing"""	18011	protein-coding gene	gene with protein product						12105228	Standard	NM_018159		Approved	DIPP3b, FLJ10628, hDIPP3beta	uc010njt.3	Q96G61	OTTHUMG00000021531		X.37:g.51239296_51239309delTCCTCGAGGCAGCC		HNSCC(48;0.14)						NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN			0	139_152	-	Ovarian(276;0.236)							Q9NVN0	Translation_Start_Site	DEL	ENST00000375992.3	37		CCDS43952.1																																																																																				0.692	NUDT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056579.1			14	36						14	36	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76907782	76907784	+	In_Frame_Del	DEL	TCC	TCC	-	rs398123423|rs587780286		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:76907782_76907784delTCC	ENST00000373344.5	-	15	4591_4593	c.4377_4379delGGA	c.(4375-4380)gaggaa>gaa	p.1459_1460EE>E	ATRX_ENST00000395603.3_In_Frame_Del_p.1421_1422EE>E|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1459	Poly-Glu.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ctcctcctcttcctcctcctcct	0.389			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(4375-4380)gaa>ga		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)		,	8,3713		0,6,2,1586,535					,	-5.4	0.0			152	29,6454		0,23,6,2334,1763	no	coding,coding	ATRX	NM_138270.2,NM_000489.3	,	0,29,8,3920,2298	A1A1,A1R,A1,RR,R		0.4473,0.215,0.3626	,	,		37,10167				SO:0001651	inframe_deletion	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76907782_76907784delTCC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4377_4379delGGA	X.37:g.76907791_76907793delTCC	ENSP00000362441:p.Glu1464del					ATRX_ENST00000395603.3_In_Frame_Del_p.EE1425del|ATRX_ENST00000480283.1_5'UTR	p.EE1463del	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			15	4591_4593	-			1463			Poly-Glu.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	In_Frame_Del	DEL	ENST00000373344.5	37	c.4377_4379delGGA	CCDS14434.1																																																																																				0.389	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		10	376						10	376	---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110406206	110406208	+	In_Frame_Del	DEL	GAA	GAA	-	rs374572591		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:110406206_110406208delGAA	ENST00000372010.1	+	10	1019_1021	c.577_579delGAA	c.(577-579)gaadel	p.E197del	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_ENST00000360648.4_In_Frame_Del_p.E218del|PAK3_ENST00000262836.4_In_Frame_Del_p.E197del|PAK3_ENST00000518291.1_In_Frame_Del_p.E218del|PAK3_ENST00000446737.1_In_Frame_Del_p.E182del|PAK3_ENST00000417227.1_In_Frame_Del_p.E203del			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_ENST00000372010.1_In_Frame_Del_p.E197del|PAK3_ENST00000446737.1_In_Frame_Del_p.E182del|PAK3_ENST00000262836.4_In_Frame_Del_p.E197del|PAK3_ENST00000425146.1_In_Frame_Del_p.E182del|PAK3_ENST00000372007.4_In_Frame_Del_p.E182del|PAK3_ENST00000417227.1_In_Frame_Del_p.E203del|PAK3_ENST00000360648.4_In_Frame_Del_p.E218del|PAK3_ENST00000518291.1_In_Frame_Del_p.E218del	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		8	444						8	444	---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119694117	119694119	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:119694117_119694119delGAG	ENST00000404115.3	-	3	830_832	c.429_431delCTC	c.(427-432)tcctca>tca	p.143_144SS>S	CUL4B_ENST00000336592.6_In_Frame_Del_p.130_131SS>S|CUL4B_ENST00000371322.5_In_Frame_Del_p.125_126SS>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_ENST00000336592.6_In_Frame_Del_p.SS132del|CUL4B_ENST00000404115.3_In_Frame_Del_p.SS145del	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		9	239						9	239	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149639325	149639327	+	In_Frame_Del	DEL	CAG	CAG	-	rs374739932|rs374561693		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:149639325_149639327delCAG	ENST00000370401.2	+	4	1790_1792	c.1480_1482delCAG	c.(1480-1482)cagdel	p.Q502del	MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	502	Poly-Gln.				male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AAGCcagcaacagcagcagcagc	0.532																																						ENST00000370401.2																			3	Substitution - coding silent(3)	p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1)	kidney(3)	breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37						c.(1480-1482)del		mastermind-like domain containing 1																																				SO:0001651	inframe_deletion	10046				male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chrX:149639325_149639327delCAG	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1480_1482delCAG	X.37:g.149639334_149639336delCAG	ENSP00000359428:p.Gln502del					MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del|MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del	p.Q502del			Q13495	MAMD1_HUMAN			4	1790_1792	+	Acute lymphoblastic leukemia(192;6.56e-05)		502			Poly-Gln.		B2RCQ4|B4DG93|B9EGA5	In_Frame_Del	DEL	ENST00000370401.2	37	c.1480_1482delCAG	CCDS14693.2																																																																																				0.532	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		10	249						10	249	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150817142	150817144	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	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	508						12	508	---	---	---	---
UBL4A	8266	broad.mit.edu	37	X	153714159	153714160	+	Frame_Shift_Ins	INS	-	-	G	rs150392222		TCGA-HZ-8519-01A-11D-2396-08	TCGA-HZ-8519-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a5e71fad-3b79-47f8-b3c7-3aa289972191	63b831aa-a874-4e47-b5e9-b75522bb6e66	g.chrX:153714159_153714160insG	ENST00000369660.4	-	3	398_399	c.313_314insC	c.(313-315)cgcfs	p.R105fs	UBL4A_ENST00000369653.4_Frame_Shift_Ins_p.R105fs|UBL4A_ENST00000477777.1_5'UTR	NM_014235.3	NP_055050.1	P11441	UBL4A_HUMAN	ubiquitin-like 4A	105					cellular protein modification process (GO:0006464)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)	small conjugating protein ligase activity (GO:0019787)			endometrium(5)|lung(1)|urinary_tract(1)	7	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ACTGAAGTGGCGGGCCAAGACT	0.629																																					Esophageal Squamous(74;88 1215 11149 34177 46777)	ENST00000369660.4																			0				endometrium(5)|lung(1)|urinary_tract(1)	7						c.(313-315)ccafs		ubiquitin-like 4A				15,3700		0,11,4,1578,533						2.0	0.8			85	29,6441		0,25,4,2328,1760	no	frameshift	UBL4A	NM_014235.3		0,36,8,3906,2293	A1A1,A1R,A1,RR,R		0.4482,0.4038,0.432				44,10141				SO:0001589	frameshift_variant	8266				protein modification process|tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	small conjugating protein ligase activity	g.chrX:153714159_153714160insG	J03589	CCDS14754.1	Xq28	2010-08-05	2005-09-27	2005-09-27	ENSG00000102178	ENSG00000102178			12505	protein-coding gene	gene with protein product		312070	"""ubiquitin-like 4"""	UBL4		2829204, 16872915	Standard	NM_014235		Approved	GDX, DXS254E, GET5, MDY2, TMA24	uc004flo.3	P11441	OTTHUMG00000013370	ENST00000369660.4:c.314dupC	X.37:g.153714162_153714162dupG	ENSP00000358674:p.Arg105fs					UBL4A_ENST00000477777.1_5'UTR|UBL4A_ENST00000369653.4_Frame_Shift_Ins_p.P105fs	p.P105fs	NM_014235.3	NP_055050.1	P11441	UBL4A_HUMAN			3	398_399	-	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)		105					Q5HY80	Frame_Shift_Ins	INS	ENST00000369660.4	37	c.313_314insC	CCDS14754.1																																																																																				0.629	UBL4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037238.2	NM_014235		10	615						10	615	---	---	---	---
