#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
ATRX	546	broad.mit.edu	37	X	76875970	76875970	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chrX:76875970T>C	ENST00000373344.5	-	20	5379	c.5165A>G	c.(5164-5166)cAt>cGt	p.H1722R	ATRX_ENST00000395603.3_Missense_Mutation_p.H1684R|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1722	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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						TTTTAGAATATGGCCTTCATC	0.294			"""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.(5164-5166)cAt>cGt		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						60.0	50.0	54.0					X																	76875970		2201	4293	6494	SO:0001583	missense	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:76875970T>C	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.5165A>G	X.37:g.76875970T>C	ENSP00000362441:p.His1722Arg					ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.H1684R	p.H1722R	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			20	5379	-			1722			Helicase ATP-binding.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	c.5165A>G	CCDS14434.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.08|18.08	3.543008|3.543008	0.65198|0.65198	.|.	.|.	ENSG00000085224|ENSG00000085224	ENST00000373344;ENST00000395603|ENST00000400866	D;D|.	0.98313|.	-4.86;-4.86|.	4.47|4.47	4.47|4.47	0.54385|0.54385	DEAD-like helicase (2);SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88584|0.88584	0.6476|0.6476	H|H	0.98996|0.98996	4.395|4.395	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.996;1.0|.	D;D|.	0.91635|.	0.99;0.999|.	D|D	0.92323|0.92323	0.5867|0.5867	10|5	0.87932|.	D|.	0|.	-9.4638|-9.4638	13.0248|13.0248	0.58808|0.58808	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1684;1722|.	P46100-4;P46100|.	.;ATRX_HUMAN|.	R|V	1722;1684|11	ENSP00000362441:H1722R;ENSP00000378967:H1684R|.	ENSP00000362441:H1722R|.	H|I	-|-	2|1	0|0	ATRX|ATRX	76762626|76762626	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.765000|0.765000	0.43378|0.43378	7.623000|7.623000	0.83113|0.83113	1.442000|1.442000	0.47568|0.47568	0.441000|0.441000	0.28932|0.28932	CAT|ATA		0.294	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		4	7	0	0	0	1	0	4	7				
AGAP3	116988	broad.mit.edu	37	7	150815375	150815375	+	Missense_Mutation	SNP	C	C	A			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr7:150815375C>A	ENST00000463381.1	+	6	597	c.101C>A	c.(100-102)aCc>aAc	p.T34N	AGAP3_ENST00000476375.1_3'UTR|AGAP3_ENST00000473312.1_Missense_Mutation_p.T262N|AGAP3_ENST00000397238.2_Missense_Mutation_p.T262N|AGAP3_ENST00000479901.1_Missense_Mutation_p.T262N|AGAP3_ENST00000335367.3_Missense_Mutation_p.T442N	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	226					cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						AAGCGGTGCACCTACTATGAG	0.642																																						ENST00000397238.2																			0				central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						c.(784-786)aCc>aAc		ArfGAP with GTPase domain, ankyrin repeat and PH domain 3							74.0	84.0	80.0					7																	150815375		2147	4278	6425	SO:0001583	missense	116988				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding	g.chr7:150815375C>A	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16923	protein-coding gene	gene with protein product			"""centaurin, gamma 3"""	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.101C>A	7.37:g.150815375C>A	ENSP00000418016:p.Thr34Asn					AGAP3_ENST00000473312.1_Missense_Mutation_p.T262N|AGAP3_ENST00000463381.1_Missense_Mutation_p.T34N|AGAP3_ENST00000479901.1_Missense_Mutation_p.T262N|AGAP3_ENST00000335367.3_Missense_Mutation_p.T442N|AGAP3_ENST00000476375.1_3'UTR	p.T262N	NM_031946.4	NP_114152.3	Q96P47	AGAP3_HUMAN			6	785	+			226			Small GTPase-like.		B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	37	c.785C>A		.	.	.	.	.	.	.	.	.	.	C	17.53	3.412150	0.62511	.	.	ENSG00000133612	ENST00000463381;ENST00000473312;ENST00000479901;ENST00000397238;ENST00000335355;ENST00000335367;ENST00000468796	T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37	4.03	4.03	0.46877	.	0.258790	0.36972	N	0.002306	T	0.55289	0.1911	M	0.65498	2.005	0.80722	D	1	P;P;D;P;D	0.65815	0.656;0.922;0.995;0.89;0.991	B;P;P;B;P	0.62885	0.443;0.634;0.833;0.363;0.908	T	0.61407	-0.7069	10	0.66056	D	0.02	.	15.3475	0.74350	0.0:1.0:0.0:0.0	.	262;442;262;262;34	C9J975;E7ESL9;Q96P47-4;E9PAL8;B3KNZ8	.;.;.;.;.	N	34;262;262;262;226;442;27	ENSP00000418016:T34N;ENSP00000418921:T262N;ENSP00000418125:T262N;ENSP00000380413:T262N;ENSP00000335589:T442N;ENSP00000418159:T27N	ENSP00000334157:T226N	T	+	2	0	AGAP3	150446308	0.978000	0.34361	1.000000	0.80357	0.010000	0.07245	2.496000	0.45346	2.087000	0.62958	0.313000	0.20887	ACC		0.642	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		33	94	1	0	4.34311e-12	1	5.24168e-12	33	94				
CLCNKA	1187	broad.mit.edu	37	1	16359720	16359720	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr1:16359720G>A	ENST00000331433.4	+	19	2004	c.1985G>A	c.(1984-1986)gGc>gAc	p.G662D	CLCNKA_ENST00000375692.1_Missense_Mutation_p.G661D|CLCNKA_ENST00000420078.1_Missense_Mutation_p.G661D|CLCNKA_ENST00000439316.2_Missense_Mutation_p.G619D|CLCNKA_ENST00000464764.1_3'UTR			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	662	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)	p.G662V(1)		breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	ACATCGCGGGGCAGAGCTGTG	0.607											OREG0013132	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000375692.1																			1	Substitution - Missense(1)	p.G662V(1)	breast(1)	breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19						c.(1981-1983)gGc>gAc		chloride channel, voltage-sensitive Ka	Niflumic Acid(DB04552)						168.0	149.0	155.0					1																	16359720		2203	4300	6503	SO:0001583	missense	0				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity	g.chr1:16359720G>A		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1985G>A	1.37:g.16359720G>A	ENSP00000332771:p.Gly662Asp		OREG0013132	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	709	CLCNKA_ENST00000331433.4_Missense_Mutation_p.G662D|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000439316.2_Missense_Mutation_p.G619D|CLCNKA_ENST00000420078.1_Missense_Mutation_p.G661D	p.G661D			P51800	CLCKA_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	20	2110	+		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)	662			CBS 2.		B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	c.1982G>A	CCDS167.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.785328	0.70337	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87	3.02	3.02	0.34903	Cystathionine beta-synthase, core (2);	0.000000	0.85682	D	0.000000	D	0.94866	0.8341	M	0.86953	2.85	0.54753	D	0.999981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.94710	0.7891	10	0.87932	D	0	.	9.6459	0.39868	0.0:0.0:1.0:0.0	.	619;661;662	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	D	661;661;619;662	ENSP00000364844:G661D;ENSP00000410353:G661D;ENSP00000414445:G619D;ENSP00000332771:G662D	ENSP00000332771:G662D	G	+	2	0	CLCNKA	16232307	1.000000	0.71417	0.992000	0.48379	0.916000	0.54674	5.803000	0.69129	1.674000	0.50907	0.313000	0.20887	GGC		0.607	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			4	231	0	0	0	1	0	4	231				
KIF15	56992	broad.mit.edu	37	3	44853776	44853776	+	Missense_Mutation	SNP	C	C	A			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr3:44853776C>A	ENST00000326047.4	+	18	2421	c.2272C>A	c.(2272-2274)Cag>Aag	p.Q758K	KIF15_ENST00000425755.1_Missense_Mutation_p.Q393K	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	758					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TACCCAAATGCAGGAGGTGAG	0.423																																						ENST00000326047.4																			0				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36						c.(2272-2274)Cag>Aag		kinesin family member 15							109.0	97.0	101.0					3																	44853776		2203	4300	6503	SO:0001583	missense	56992				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity	g.chr3:44853776C>A	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.2272C>A	3.37:g.44853776C>A	ENSP00000324020:p.Gln758Lys					KIF15_ENST00000425755.1_Missense_Mutation_p.Q393K	p.Q758K	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)	18	2421	+			758					Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	c.2272C>A	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001056	0.54254	.	.	ENSG00000163808	ENST00000326047;ENST00000481166;ENST00000396031;ENST00000425755	T;T;T	0.48836	0.8;0.8;0.8	5.81	5.81	0.92471	.	0.000000	0.48767	D	0.000167	T	0.46927	0.1418	M	0.70595	2.14	0.32993	D	0.52523	P;P	0.38473	0.524;0.633	B;B	0.34489	0.084;0.184	T	0.59542	-0.7435	10	0.23891	T	0.37	.	16.3403	0.83080	0.0:0.8682:0.1318:0.0	.	393;758	C9JKA9;Q9NS87	.;KIF15_HUMAN	K	758;530;757;393	ENSP00000324020:Q758K;ENSP00000425499:Q530K;ENSP00000389982:Q393K	ENSP00000324020:Q758K	Q	+	1	0	KIF15	44828780	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	3.246000	0.51414	2.756000	0.94617	0.655000	0.94253	CAG		0.423	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			3	39	1	0	1	1	1	3	39				
PSMG1	8624	broad.mit.edu	37	21	40552362	40552362	+	Splice_Site	SNP	G	G	C	rs200021987		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr21:40552362G>C	ENST00000331573.3	-	3	707	c.242C>G	c.(241-243)gCa>gGa	p.A81G	PSMG1_ENST00000380900.2_Splice_Site_p.A81G	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	81					cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				TGACAGAAATGCTGTAAAAAA	0.358																																						ENST00000331573.3																			0				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8						c.e3-1		proteasome (prosome, macropain) assembly chaperone 1		G	GLY/ALA,GLY/ALA	0,4406		0,0,2203	77.0	72.0	74.0		242,242	4.9	1.0	21		74	2,8598	2.2+/-6.3	0,2,4298	yes	missense-near-splice,missense-near-splice	PSMG1	NM_003720.2,NM_203433.1	60,60	0,2,6501	CC,CG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	81/289,81/268	40552362	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	8624				proteasome assembly	endoplasmic reticulum	protein binding	g.chr21:40552362G>C	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"""Down syndrome critical region gene 2"""	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.242-1C>G	21.37:g.40552362G>C						PSMG1_ENST00000380900.2_Splice_Site_p.A81_splice	p.A81_splice	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN			3	707	-		Prostate(19;8.44e-08)	81					B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Splice_Site	SNP	ENST00000331573.3	37	c.241_splice	CCDS13660.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.69|17.69	3.451647|3.451647	0.63290|0.63290	0.0|0.0	2.33E-4|2.33E-4	ENSG00000183527|ENSG00000183527	ENST00000331573;ENST00000380900|ENST00000440607	T;T|.	0.19394|.	2.15;2.15|.	5.78|5.78	4.9|4.9	0.64082|0.64082	.|.	0.252729|.	0.39687|.	N|.	0.001291|.	T|T	0.46946|0.46946	0.1419|0.1419	L|L	0.38649|0.38649	1.16|1.16	0.38838|0.38838	D|D	0.956001|0.956001	B;D|.	0.89917|.	0.181;1.0|.	B;D|.	0.83275|.	0.074;0.996|.	T|T	0.41161|0.41161	-0.9524|-0.9524	10|6	0.06757|0.02654	T|T	0.87|1	.|.	11.8567|11.8567	0.52441|0.52441	0.0813:0.0:0.9187:0.0|0.0813:0.0:0.9187:0.0	.|.	81;81|.	O95456-2;O95456|.	.;PSMG1_HUMAN|.	G|R	81|1	ENSP00000329915:A81G;ENSP00000370286:A81G|.	ENSP00000329915:A81G|ENSP00000398569:S45R	A|S	-|-	2|3	0|2	PSMG1|PSMG1	39474232|39474232	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.619000|0.619000	0.37552|0.37552	5.914000|5.914000	0.69964|0.69964	1.444000|1.444000	0.47605|0.47605	0.557000|0.557000	0.71058|0.71058	GCA|AGC		0.358	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720	Missense_Mutation	20	57	0	0	0	1	0	20	57				
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	lincRNA	SNP	C	C	T	rs367060	byFrequency	TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTCAGCCTTCCGCCGGGCCAG	0.672													.|||	253	0.0505192	0.115	0.0533	5008	,	,		65734	0.0119		0.0437	False		,,,				2504	0.0082					ENST00000412962.1																			0																																																			0							g.chr1:16946434C>T	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946434C>T														0	1085	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		3	10	0	0	0	1	0	3	10				
ZFYVE9	9372	broad.mit.edu	37	1	52704261	52704261	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr1:52704261A>G	ENST00000371591.1	+	3	1303	c.1172A>G	c.(1171-1173)gAg>gGg	p.E391G	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.E391G|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.E391G	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	391					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						AATATGACAGAGCATTTCTCT	0.363																																						ENST00000287727.3																			0				breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						c.(1171-1173)gAg>gGg		zinc finger, FYVE domain containing 9							76.0	74.0	75.0					1																	52704261		2203	4300	6503	SO:0001583	missense	9372				endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity	g.chr1:52704261A>G	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1172A>G	1.37:g.52704261A>G	ENSP00000360647:p.Glu391Gly					ZFYVE9_ENST00000371591.1_Missense_Mutation_p.E391G|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.E391G|ZFYVE9_ENST00000361625.1_Missense_Mutation_p.E391G	p.E391G	NM_004799.2	NP_004790.2	O95405	ZFYV9_HUMAN			4	1344	+			391					Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	c.1172A>G	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	5.910	0.351931	0.11182	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.57595	0.88;0.39;0.89;0.89	4.69	2.3	0.28687	.	0.000000	0.47455	D	0.000236	T	0.31918	0.0812	N	0.19112	0.55	0.09310	N	0.999997	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.11329	0.001;0.0;0.006	T	0.14643	-1.0465	10	0.44086	T	0.13	.	5.3683	0.16125	0.72:0.0:0.1504:0.1296	.	391;391;391	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	G	391	ENSP00000349737:E391G;ENSP00000355358:E391G;ENSP00000287727:E391G;ENSP00000360647:E391G	ENSP00000287727:E391G	E	+	2	0	ZFYVE9	52476849	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	2.356000	0.44116	0.834000	0.34852	-0.261000	0.10672	GAG		0.363	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		15	83	0	0	0	1	0	15	83				
CFAP69	79846	broad.mit.edu	37	7	89874847	89874847	+	Missense_Mutation	SNP	G	G	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr7:89874847G>T	ENST00000389297.4	+	1	360	c.109G>T	c.(109-111)Gat>Tat	p.D37Y	C7orf63_ENST00000316089.8_Missense_Mutation_p.D37Y|C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000497910.1_Missense_Mutation_p.D37Y	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		37										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GACGGAGGACGATGAGGCGCA	0.627																																						ENST00000389297.4																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						c.(109-111)Gat>Tat		chromosome 7 open reading frame 63							125.0	140.0	135.0					7																	89874847		2050	4207	6257	SO:0001583	missense	79846						binding	g.chr7:89874847G>T																												ENST00000389297.4:c.109G>T	7.37:g.89874847G>T	ENSP00000373948:p.Asp37Tyr					C7orf63_ENST00000497910.1_Missense_Mutation_p.D37Y|C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000316089.8_Missense_Mutation_p.D37Y	p.D37Y	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN			1	360	+			37					A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	c.109G>T	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	2.117	-0.402303	0.04865	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910	T;T;T	0.19806	2.12;2.12;2.12	4.44	2.61	0.31194	.	.	.	.	.	T	0.12433	0.0302	N	0.08118	0	0.09310	N	1	B;P;P	0.46142	0.112;0.785;0.873	B;B;B	0.42692	0.084;0.395;0.287	T	0.12477	-1.0546	9	0.52906	T	0.07	0.0012	9.8595	0.41105	0.185:0.0:0.815:0.0	.	37;37;37	A5D8W1-5;A5D8W1;A5D8W1-4	.;CG063_HUMAN;.	Y	37	ENSP00000373948:D37Y;ENSP00000321753:D37Y;ENSP00000419549:D37Y	ENSP00000321753:D37Y	D	+	1	0	C7orf63	89712783	0.019000	0.18553	0.001000	0.08648	0.019000	0.09904	0.629000	0.24538	0.230000	0.21059	-1.814000	0.00607	GAT		0.627	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			4	173	1	0	0.00116845	1	0.00131921	4	173				
OR5M10	390167	broad.mit.edu	37	11	56344882	56344882	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr11:56344882C>T	ENST00000526812.2	-	1	381	c.316G>A	c.(316-318)Gcc>Acc	p.A106T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						ATCACTAGGGCGATGAAGAGA	0.438																																						ENST00000526812.2																			0				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						c.(316-318)Gcc>Acc		olfactory receptor, family 5, subfamily M, member 10							167.0	152.0	157.0					11																	56344882		1993	4175	6168	SO:0001583	missense	390167				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:56344882C>T	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.316G>A	11.37:g.56344882C>T	ENSP00000436004:p.Ala106Thr						p.A106T	NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN			1	381	-			106					B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	c.316G>A	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	C	0.516	-0.864144	0.02590	.	.	ENSG00000254834	ENST00000526812	T	0.02140	4.43	4.04	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01661	0.0053	N	0.20530	0.585	0.09310	N	1	B	0.19073	0.033	B	0.15052	0.012	T	0.48937	-0.8990	9	0.25751	T	0.34	.	5.5077	0.16864	0.1613:0.656:0.0:0.1826	.	106	Q6IEU7	OR5MA_HUMAN	T	106	ENSP00000436004:A106T	ENSP00000436004:A106T	A	-	1	0	OR5M10	56101458	0.000000	0.05858	0.684000	0.30055	0.011000	0.07611	-0.868000	0.04236	0.435000	0.26365	0.632000	0.83419	GCC		0.438	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		14	61	0	0	0	1	0	14	61				
LRRC8C	84230	broad.mit.edu	37	1	90178874	90178874	+	Missense_Mutation	SNP	A	A	G	rs558056157		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr1:90178874A>G	ENST00000370454.4	+	3	1000	c.745A>G	c.(745-747)Agg>Ggg	p.R249G	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	249					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		GAAGAAGTTCAGGCTGCATGT	0.403																																						ENST00000370454.4																			0				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28						c.(745-747)Agg>Ggg		leucine rich repeat containing 8 family, member C							106.0	107.0	107.0					1																	90178874		2203	4300	6503	SO:0001583	missense	84230					endoplasmic reticulum membrane|integral to membrane		g.chr1:90178874A>G		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.745A>G	1.37:g.90178874A>G	ENSP00000359483:p.Arg249Gly					RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	p.R249G	NM_032270.4	NP_115646.2	Q8TDW0	LRC8C_HUMAN		all cancers(265;0.00756)|Epithelial(280;0.0313)	3	1000	+		all_lung(203;0.126)	249					B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	c.745A>G	CCDS725.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.818795	0.50633	.	.	ENSG00000171488	ENST00000370454	T	0.30981	1.51	6.05	0.581	0.17407	.	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.79123	2.44	0.52501	D	0.99995	D	0.89917	1.0	D	0.91635	0.999	T	0.61758	-0.6997	10	0.87932	D	0	.	17.3411	0.87296	0.3426:0.6574:0.0:0.0	.	249	Q8TDW0	LRC8C_HUMAN	G	249	ENSP00000359483:R249G	ENSP00000359483:R249G	R	+	1	2	LRRC8C	89951462	0.943000	0.32029	1.000000	0.80357	0.998000	0.95712	0.568000	0.23623	0.122000	0.18314	0.528000	0.53228	AGG		0.403	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		4	96	0	0	0	1	0	4	96				
NALCN	259232	broad.mit.edu	37	13	101797192	101797192	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr13:101797192C>T	ENST00000251127.6	-	16	1976	c.1895G>A	c.(1894-1896)cGa>cAa	p.R632Q		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	632					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTCAAAGATTCGCAGGCGTAA	0.348																																						ENST00000251127.6																			0				NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177						c.(1894-1896)cGa>cAa		sodium leak channel, non-selective							172.0	190.0	184.0					13																	101797192		2203	4300	6503	SO:0001583	missense	259232					integral to membrane	sodium channel activity|voltage-gated ion channel activity	g.chr13:101797192C>T	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1895G>A	13.37:g.101797192C>T	ENSP00000251127:p.Arg632Gln						p.R632Q	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN			16	1976	-	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		632					Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	c.1895G>A	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	36	5.738529	0.96865	.	.	ENSG00000102452	ENST00000251127	D	0.98028	-4.67	5.75	5.75	0.90469	.	0.061578	0.64402	D	0.000003	D	0.96809	0.8958	L	0.38175	1.15	0.80722	D	1	D	0.60160	0.987	P	0.50405	0.64	D	0.96377	0.9278	10	0.42905	T	0.14	.	19.9417	0.97165	0.0:1.0:0.0:0.0	.	632	Q8IZF0	NALCN_HUMAN	Q	632	ENSP00000251127:R632Q	ENSP00000251127:R632Q	R	-	2	0	NALCN	100595193	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.398000	0.79919	2.720000	0.93068	0.655000	0.94253	CGA		0.348	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		89	187	0	0	0	1	0	89	187				
TRPM7	54822	broad.mit.edu	37	15	50886773	50886773	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr15:50886773C>T	ENST00000313478.7	-	24	3609	c.3328G>A	c.(3328-3330)Gta>Ata	p.V1110I	TRPM7_ENST00000560955.1_Missense_Mutation_p.V1110I	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1110					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TACTTCCATACAATATTGGAA	0.299																																						ENST00000313478.7																			0				breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52						c.(3328-3330)Gta>Ata		transient receptor potential cation channel, subfamily M, member 7							80.0	73.0	75.0					15																	50886773		1827	4075	5902	SO:0001583	missense	54822				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity	g.chr15:50886773C>T	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.3328G>A	15.37:g.50886773C>T	ENSP00000320239:p.Val1110Ile					TRPM7_ENST00000560955.1_Missense_Mutation_p.V1110I	p.V1110I	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN		all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)	24	3609	-			1110					Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	c.3328G>A	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036002	0.54896	.	.	ENSG00000092439	ENST00000313478	T	0.50277	0.75	5.53	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.38241	0.1033	L	0.37800	1.135	0.54753	D	0.999988	P	0.37636	0.603	B	0.32762	0.152	T	0.21042	-1.0257	10	0.40728	T	0.16	-18.119	16.4704	0.84109	0.0:0.8688:0.1312:0.0	.	1110	Q96QT4	TRPM7_HUMAN	I	1110	ENSP00000320239:V1110I	ENSP00000320239:V1110I	V	-	1	0	TRPM7	48674065	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.887000	0.63156	1.310000	0.45006	0.655000	0.94253	GTA		0.299	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		14	19	0	0	0	1	0	14	19				
RP11-24M17.5	0	broad.mit.edu	37	15	76074431	76074431	+	RNA	SNP	C	C	T	rs371238897		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr15:76074431C>T	ENST00000395215.3	+	0	610																		p.S190L(2)									CTCCAGTCCTCGAGCTGCAGA	0.547																																						ENST00000395215.3																			2	Substitution - Missense(2)	p.S190L(2)	endometrium(2)																																																0							g.chr15:76074431C>T																													15.37:g.76074431C>T														0	610	+									RNA	SNP	ENST00000395215.3	37			.	.	.	.	.	.	.	.	.	.	.	3.205	-0.162863	0.06502	.	.	ENSG00000187812	ENST00000395215	.	.	.	0.789	0.789	0.18607	.	.	.	.	.	T	0.29850	0.0746	.	.	.	.	.	.	B	0.20550	0.046	B	0.15870	0.014	T	0.30208	-0.9986	6	0.27082	T	0.32	.	7.4893	0.27452	0.0:0.9999:0.0:1.0E-4	.	190	B4DZE6	.	L	190	.	ENSP00000378641:S190L	S	+	2	0	AC019294.2	73861486	0.987000	0.35691	0.013000	0.15412	0.024000	0.10985	3.310000	0.51911	0.745000	0.32763	0.274000	0.19336	TCG		0.547	RP11-24M17.5-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000420501.1			4	32	0	0	0	1	0	4	32				
LRRTM1	347730	broad.mit.edu	37	2	80530285	80530285	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr2:80530285G>C	ENST00000295057.3	-	2	1316	c.660C>G	c.(658-660)gaC>gaG	p.D220E	CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000361291.4_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.D220E|CTNNA2_ENST00000466387.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	220					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CCTTGACCAAGTCGTTGTGCT	0.572										HNSCC(69;0.2)																												ENST00000295057.3																			0				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						c.(658-660)gaC>gaG		leucine rich repeat transmembrane neuronal 1							116.0	111.0	113.0					2																	80530285		2203	4300	6503	SO:0001583	missense	347730					axon|endoplasmic reticulum membrane|growth cone|integral to membrane		g.chr2:80530285G>C	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.660C>G	2.37:g.80530285G>C	ENSP00000295057:p.Asp220Glu	HNSCC(69;0.2)				CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.D220E	p.D220E	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN			2	1316	-			220					A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	c.660C>G	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.357450	0.24598	.	.	ENSG00000162951	ENST00000295057;ENST00000409148;ENST00000416268	T;T;T	0.79454	-1.27;-1.27;4.35	5.26	1.41	0.22369	.	0.056942	0.64402	U	0.000002	T	0.47432	0.1445	N	0.01800	-0.715	0.44110	D	0.996881	B	0.06786	0.001	B	0.10450	0.005	T	0.15752	-1.0426	9	.	.	.	.	9.589	0.39534	0.2873:0.0:0.7127:0.0	.	220	Q86UE6	LRRT1_HUMAN	E	220	ENSP00000295057:D220E;ENSP00000386646:D220E;ENSP00000415368:D220E	.	D	-	3	2	LRRTM1	80383796	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	0.719000	0.25881	0.201000	0.20466	0.655000	0.94253	GAC		0.572	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		11	124	0	0	0	1	0	11	124				
ZDBF2	57683	broad.mit.edu	37	2	207171520	207171520	+	Silent	SNP	G	G	A			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr2:207171520G>A	ENST00000374423.3	+	5	2654	c.2268G>A	c.(2266-2268)ccG>ccA	p.P756P		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	756							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ATTCTGACCCGCCTCTTCTGT	0.418																																						ENST00000374423.3																			0				endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						c.(2266-2268)ccG>ccA		zinc finger, DBF-type containing 2							185.0	188.0	187.0					2																	207171520		1899	4092	5991	SO:0001819	synonymous_variant	57683						nucleic acid binding|zinc ion binding	g.chr2:207171520G>A	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2268G>A	2.37:g.207171520G>A							p.P756P	NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN			5	2654	+			756					Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	c.2268G>A	CCDS46501.1																																																																																				0.418	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		4	197	0	0	0	1	0	4	197				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			28	49	0	0	0	1	0	28	49				
FADS3	3995	broad.mit.edu	37	11	61644404	61644404	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr11:61644404C>T	ENST00000278829.2	-	8	1069	c.917G>A	c.(916-918)cGc>cAc	p.R306H	FADS3_ENST00000525588.1_Missense_Mutation_p.R278H|FADS3_ENST00000540820.1_Missense_Mutation_p.R306H|FADS3_ENST00000527697.1_Missense_Mutation_p.R182H	NM_021727.3	NP_068373.1	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	306					unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TAAGAAGAAGCGGGCATAGAA	0.622																																						ENST00000540820.1																			0				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						c.(916-918)cGc>cAc		fatty acid desaturase 3							86.0	78.0	81.0					11																	61644404		2195	4294	6489	SO:0001583	missense	3995				electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	heme binding|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water	g.chr11:61644404C>T		CCDS8013.1	11q12-q13.1	2013-01-25			ENSG00000221968	ENSG00000221968	1.14.19.3	"""Fatty acid desaturases"""	3576	protein-coding gene	gene with protein product	"""delta-9-desaturase"""	606150		LLCDL3			Standard	NM_021727		Approved	CYB5RP	uc001nsm.3	Q9Y5Q0	OTTHUMG00000167500	ENST00000278829.2:c.917G>A	11.37:g.61644404C>T	ENSP00000278829:p.Arg306His					FADS3_ENST00000527697.1_Missense_Mutation_p.R182H|FADS3_ENST00000525588.1_Missense_Mutation_p.R278H|FADS3_ENST00000278829.2_Missense_Mutation_p.R306H	p.R306H			Q9Y5Q0	FADS3_HUMAN			8	989	-			306					O60426	Missense_Mutation	SNP	ENST00000278829.2	37	c.917G>A	CCDS8013.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	29.8|29.8	5.036134|5.036134	0.93630|0.93630	.|.	.|.	ENSG00000221968|ENSG00000221968	ENST00000527379|ENST00000527697;ENST00000278829;ENST00000540820;ENST00000525588;ENST00000531956;ENST00000534223	.|T;T;T;T;T;T	.|0.78126	.|-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Fatty acid desaturase, type 1 (1);	.|.	.|.	.|.	.|.	T|T	0.79811|0.79811	0.4510|0.4510	M|M	0.74389|0.74389	2.26|2.26	0.58432|0.58432	D|D	0.999999|0.999999	.|P;P	.|0.42757	.|0.789;0.574	.|P;B	.|0.45428	.|0.48;0.364	T|T	0.76672|0.76672	-0.2873|-0.2873	5|9	.|0.15499	.|T	.|0.54	-20.6504|-20.6504	15.9165|15.9165	0.79524|0.79524	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|182;306	.|E9PKP8;Q9Y5Q0	.|.;FADS3_HUMAN	T|H	81|182;306;306;278;182;182	.|ENSP00000431533:R182H;ENSP00000278829:R306H;ENSP00000439308:R306H;ENSP00000432206:R278H;ENSP00000436890:R182H;ENSP00000434551:R182H	.|ENSP00000278829:R306H	A|R	-|-	1|2	0|0	FADS3|FADS3	61400980|61400980	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.997000|0.997000	0.91878|0.91878	6.225000|6.225000	0.72271|0.72271	2.530000|2.530000	0.85305|0.85305	0.549000|0.549000	0.68633|0.68633	GCT|CGC		0.622	FADS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394836.1			3	5	0	0	0	1	0	3	5				
ITFG3	83986	broad.mit.edu	37	16	312148	312148	+	Silent	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr16:312148C>T	ENST00000399932.3	+	7	1216	c.765C>T	c.(763-765)agC>agT	p.S255S	ITFG3_ENST00000442458.2_Silent_p.S255S|ITFG3_ENST00000600536.1_Silent_p.S255S|ITFG3_ENST00000301679.2_Silent_p.S255S|ITFG3_ENST00000301678.3_Silent_p.S255S|ITFG3_ENST00000450082.2_Silent_p.S255S	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	255						cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				TCAGAGGCAGCCTTGGTGTGG	0.587																																						ENST00000399932.3																			0				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16						c.(763-765)agC>agT		integrin alpha FG-GAP repeat containing 3							53.0	61.0	58.0					16																	312148		2175	4272	6447	SO:0001819	synonymous_variant	83986					integral to membrane		g.chr16:312148C>T	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 9"""	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.765C>T	16.37:g.312148C>T						ITFG3_ENST00000442458.2_Silent_p.S255S|ITFG3_ENST00000450082.2_Silent_p.S255S|ITFG3_ENST00000301678.3_Silent_p.S255S|ITFG3_ENST00000301679.2_Silent_p.S255S|ITFG3_ENST00000600536.1_Silent_p.S255S	p.S255S			Q9H0X4	ITFG3_HUMAN			7	1216	+		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)	255					D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Silent	SNP	ENST00000399932.3	37	c.765C>T	CCDS10402.1																																																																																				0.587	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039		17	33	0	0	0	1	0	17	33				
RP1	6101	broad.mit.edu	37	8	55541829	55541829	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr8:55541829C>T	ENST00000220676.1	+	4	5535	c.5387C>T	c.(5386-5388)aCg>aTg	p.T1796M		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1796					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.T1796M(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CCAGGCCCAACGATGGATGAA	0.448																																					Colon(91;1014 1389 7634 14542 40420)	ENST00000220676.1																			1	Substitution - Missense(1)	p.T1796M(1)	endometrium(1)	NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169						c.(5386-5388)aCg>aTg		retinitis pigmentosa 1 (autosomal dominant)							77.0	74.0	75.0					8																	55541829		2203	4300	6503	SO:0001583	missense	6101				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding	g.chr8:55541829C>T	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5387C>T	8.37:g.55541829C>T	ENSP00000220676:p.Thr1796Met						p.T1796M	NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		4	5535	+		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	1796						Missense_Mutation	SNP	ENST00000220676.1	37	c.5387C>T	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	9.173	1.021724	0.19433	.	.	ENSG00000104237	ENST00000220676	T	0.21191	2.02	5.93	-7.18	0.01505	.	1.642690	0.03391	N	0.201882	T	0.15132	0.0365	L	0.36672	1.1	0.09310	N	1	B	0.31968	0.349	B	0.31191	0.125	T	0.23762	-1.0179	10	0.66056	D	0.02	.	7.0392	0.25010	0.1497:0.3819:0.3642:0.1042	.	1796	P56715	RP1_HUMAN	M	1796	ENSP00000220676:T1796M	ENSP00000220676:T1796M	T	+	2	0	RP1	55704382	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.201000	0.17276	-1.915000	0.01077	-2.053000	0.00404	ACG		0.448	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		8	12	0	0	0	1	0	8	12				
NEURL1	9148	broad.mit.edu	37	10	105331484	105331484	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr10:105331484C>T	ENST00000369780.4	+	3	963	c.554C>T	c.(553-555)tCg>tTg	p.S185L	NEURL_ENST00000465048.1_3'UTR|NEURL_ENST00000369777.2_Missense_Mutation_p.S168L	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		185	NHR 1. {ECO:0000255|PROSITE- ProRule:PRU00400}.				brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		ATCAACGACTCGGCTGTTATG	0.632																																						ENST00000369780.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17						c.(553-555)tCg>tTg									163.0	109.0	128.0					10																	105331484		2203	4300	6503	SO:0001583	missense	0				nervous system development	perinuclear region of cytoplasm	zinc ion binding	g.chr10:105331484C>T																												ENST00000369780.4:c.554C>T	10.37:g.105331484C>T	ENSP00000358795:p.Ser185Leu					NEURL_ENST00000465048.1_3'UTR|NEURL_ENST00000369777.2_Missense_Mutation_p.S168L	p.S185L	NM_004210.4	NP_004201.3	O76050	NEU1A_HUMAN		Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)	3	963	+			185			NHR 1.		Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	37	c.554C>T	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.952769	0.73787	.	.	ENSG00000107954	ENST00000369780;ENST00000437579;ENST00000369777	T;T	0.26957	1.7;1.7	5.64	5.64	0.86602	NEUZ (1);	0.053526	0.85682	D	0.000000	T	0.23370	0.0565	L	0.50333	1.59	0.58432	D	0.999998	D	0.53745	0.962	B	0.41135	0.348	T	0.01829	-1.1265	10	0.25106	T	0.35	-14.2244	12.0702	0.53611	0.0:0.9218:0.0:0.0782	.	185	O76050	NEU1A_HUMAN	L	185;168;168	ENSP00000358795:S185L;ENSP00000358792:S168L	ENSP00000358792:S168L	S	+	2	0	NEURL	105321474	0.996000	0.38824	0.911000	0.35937	0.920000	0.55202	3.282000	0.51693	2.648000	0.89879	0.561000	0.74099	TCG		0.632	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			11	51	0	0	0	1	0	11	51				
USP24	23358	broad.mit.edu	37	1	55598323	55598323	+	Silent	SNP	C	C	A			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr1:55598323C>A	ENST00000294383.6	-	31	3431	c.3432G>T	c.(3430-3432)ctG>ctT	p.L1144L	USP24_ENST00000407756.1_Silent_p.L984L	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1144	Ser-rich.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						GCTTTGATGACAGGGATGGAG	0.393																																						ENST00000294383.6																			0				breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						c.(3430-3432)ctG>ctT		ubiquitin specific peptidase 24							78.0	75.0	76.0					1																	55598323		1902	4131	6033	SO:0001819	synonymous_variant	23358				ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity	g.chr1:55598323C>A	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.3432G>T	1.37:g.55598323C>A						USP24_ENST00000407756.1_Silent_p.L984L	p.L1144L	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN			31	3431	-			1144			Ser-rich.		Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	c.3432G>T	CCDS44154.2																																																																																				0.393	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			3	40	1	0	0.004672	1	0.00511	3	40				
PAG1	55824	broad.mit.edu	37	8	81897059	81897059	+	Silent	SNP	C	C	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr8:81897059C>T	ENST00000220597.4	-	7	1538	c.828G>A	c.(826-828)ggG>ggA	p.G276G		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	276					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			CCGCCTCTCCCCCTTCCTTCT	0.502																																						ENST00000220597.4																			0				breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11						c.(826-828)ggG>ggA		phosphoprotein associated with glycosphingolipid microdomains 1							114.0	103.0	107.0					8																	81897059		2203	4300	6503	SO:0001819	synonymous_variant	55824				epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity	g.chr8:81897059C>T	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.828G>A	8.37:g.81897059C>T							p.G276G	NM_018440.3	NP_060910.3	Q9NWQ8	PAG1_HUMAN	BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)		7	1538	-	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		276					A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Silent	SNP	ENST00000220597.4	37	c.828G>A	CCDS6227.1																																																																																				0.502	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		5	107	0	0	0	1	0	5	107				
TTN	7273	broad.mit.edu	37	2	179470238	179470238	+	Missense_Mutation	SNP	A	A	T			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr2:179470238A>T	ENST00000591111.1	-	229	49085	c.48861T>A	c.(48859-48861)gaT>gaA	p.D16287E	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D8988E|TTN_ENST00000460472.2_Missense_Mutation_p.D8863E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D17928E|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D9055E|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D15360E|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16287	Fibronectin type-III 18. {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)			TTTGGTGTTCATCAAGATTTT	0.393																																						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.(53782-53784)gaT>gaA		titin							121.0	115.0	117.0					2																	179470238		1909	4115	6024	SO:0001583	missense	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179470238A>T	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.48861T>A	2.37:g.179470238A>T	ENSP00000465570:p.Asp16287Glu					TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D9055E|TTN_ENST00000460472.2_Missense_Mutation_p.D8863E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D8988E|TTN_ENST00000342992.6_Missense_Mutation_p.D15360E|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.D16287E	p.D17928E	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)		279	54008	-			16287			Fibronectin type-III 29.		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	Missense_Mutation	SNP	ENST00000591111.1	37	c.53784T>A		.	.	.	.	.	.	.	.	.	.	A	11.33	1.606821	0.28623	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.74	2.17	0.27698	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.27454	0.0674	N	0.04297	-0.235	0.29626	N	0.845818	B;B;B;B	0.21071	0.051;0.051;0.051;0.051	B;B;B;B	0.19946	0.027;0.027;0.027;0.027	T	0.21109	-1.0255	9	0.87932	D	0	.	4.5667	0.12189	0.658:0.0:0.2109:0.1311	.	8863;8988;9055;16287	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	15360;8863;9055;8988;8863	ENSP00000343764:D15360E;ENSP00000434586:D8863E;ENSP00000340554:D9055E;ENSP00000352154:D8988E	ENSP00000340554:D9055E	D	-	3	2	TTN	179178483	0.930000	0.31532	1.000000	0.80357	0.977000	0.68977	0.148000	0.16224	0.461000	0.27071	-0.376000	0.06991	GAT		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		17	114	0	0	0	1	0	17	114				
LINC00971	440970	broad.mit.edu	37	3	84741480	84741480	+	lincRNA	DEL	A	A	-	rs71104976		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr3:84741480delA	ENST00000484892.1	-	0	2354					NR_033860.1				long intergenic non-protein coding RNA 971																		CCTGTCCCAGAAAAAAAAAAA	0.388																																						ENST00000484892.1																			0																																																			0							g.chr3:84741480delA			3p12.1	2013-06-07			ENSG00000242641	ENSG00000242641		"""Long non-coding RNAs"""	48737	non-coding RNA	RNA, long non-coding							Standard	NR_033860		Approved				OTTHUMG00000158981		3.37:g.84741480delA								NR_033860.1						0	2354	-									RNA	DEL	ENST00000484892.1	37																																																																																						0.388	LINC00971-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000352776.2			3	6						3	6	---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	38020014	38020014	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr4:38020014delA	ENST00000261439.4	+	4	1277	c.922delA	c.(922-924)aaafs	p.K309fs	TBC1D1_ENST00000508802.1_Frame_Shift_Del_p.K309fs	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	309	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TCCTGACACCAAAAAAATAGC	0.313																																						ENST00000261439.4																			0				NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						c.(922-924)aafs		TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1							68.0	72.0	70.0					4																	38020014		2203	4298	6501	SO:0001589	frameshift_variant	23216					nucleus	Rab GTPase activator activity	g.chr4:38020014delA	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.922delA	4.37:g.38020014delA	ENSP00000261439:p.Lys309fs					TBC1D1_ENST00000508802.1_Frame_Shift_Del_p.K309fs	p.K309fs	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN			4	1277	+			309			PID.		B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Frame_Shift_Del	DEL	ENST00000261439.4	37	c.922delA	CCDS33972.1																																																																																				0.313	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173		7	122						7	122	---	---	---	---
PPARGC1B	133522	broad.mit.edu	37	5	149216400	149216402	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr5:149216400_149216402delCAG	ENST00000309241.5	+	8	2414_2416	c.2382_2384delCAG	c.(2380-2385)gacagc>gac	p.S799del	PPARGC1B_ENST00000403750.1_In_Frame_Del_p.S735del|PPARGC1B_ENST00000394320.3_In_Frame_Del_p.S799del|PPARGC1B_ENST00000360453.4_In_Frame_Del_p.S760del	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	799	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)	p.S795N(1)		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)			TCTTTGAAGACAGCAGCAGCAGC	0.601																																						ENST00000309241.5																			1	Substitution - Missense(1)	p.S795N(1)	breast(1)	NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30						c.(2380-2385)gac>ga		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.chr5:149216400_149216402delCAG	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.2382_2384delCAG	5.37:g.149216409_149216411delCAG	ENSP00000312649:p.Ser799del					PPARGC1B_ENST00000394320.3_In_Frame_Del_p.DS794del|PPARGC1B_ENST00000360453.4_In_Frame_Del_p.DS755del|PPARGC1B_ENST00000403750.1_In_Frame_Del_p.DS730del	p.DS794del	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		8	2414_2416	+			794			Glu-rich.		A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	In_Frame_Del	DEL	ENST00000309241.5	37	c.2382_2384delCAG	CCDS4298.1																																																																																				0.601	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		9	195						9	195	---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92146721	92146721	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr7:92146721delT	ENST00000248633.4	-	5	1203	c.1108delA	c.(1108-1110)attfs	p.I370fs	PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Frame_Shift_Del_p.I370fs|PEX1_ENST00000541751.1_5'UTR	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	370					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCTGACCTAATTTTTTTTTGA	0.353																																						ENST00000248633.4																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(1108-1110)ttfs		peroxisomal biogenesis factor 1							125.0	126.0	126.0					7																	92146721		2203	4300	6503	SO:0001589	frameshift_variant	5189				microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding	g.chr7:92146721delT	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.1108delA	7.37:g.92146721delT	ENSP00000248633:p.Ile370fs					PEX1_ENST00000428214.1_Frame_Shift_Del_p.I370fs|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000541751.1_5'UTR	p.I370fs	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)		5	1203	-	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	370					A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Frame_Shift_Del	DEL	ENST00000248633.4	37	c.1108delA	CCDS5627.1																																																																																				0.353	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		12	284						12	284	---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110455173	110455174	+	Splice_Site	INS	-	-	G	rs375659563		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	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	7	133						7	133	---	---	---	---
KTN1-AS1	100129075	broad.mit.edu	37	14	56014173	56014174	+	RNA	DEL	AG	AG	-	rs375963888|rs372958232		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr14:56014173_56014174delAG	ENST00000554558.1	-	0	364							Q86SY8	KTAS1_HUMAN	KTN1 antisense RNA 1																		aaaaaaaaaaagaaTTGGCACA	0.446																																						ENST00000554558.1																			0																																																			0							g.chr14:56014173_56014174delAG			14q22.3	2012-10-12	2012-08-15	2011-12-07	ENSG00000186615	ENSG00000186615		"""Long non-coding RNAs"""	19842	non-coding RNA	RNA, long non-coding			"""chromosome 14 open reading frame 33"", ""KTN1 antisense RNA 1 (non-protein coding)"""	C14orf33			Standard	NR_027123		Approved		uc001xbz.2	Q86SY8	OTTHUMG00000171057		14.37:g.56014173_56014174delAG														0	364	-									RNA	DEL	ENST00000554558.1	37																																																																																						0.446	KTN1-AS1-004	KNOWN	basic	antisense	antisense	OTTHUMT00000411452.1	NR_027123		5	9						5	9	---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57523450	57523451	+	Frame_Shift_Ins	INS	-	-	GCAA			TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr15:57523450_57523451insGCAA	ENST00000267811.5	+	9	984_985	c.680_681insGCAA	c.(679-684)atgcaafs	p.-228fs	TCF12_ENST00000438423.2_Frame_Shift_Ins_p.-228fs|TCF12_ENST00000543579.1_Frame_Shift_Ins_p.-58fs|TCF12_ENST00000333725.5_Frame_Shift_Ins_p.-228fs|TCF12_ENST00000537840.1_Frame_Shift_Ins_p.-39fs|TCF12_ENST00000343827.3_Frame_Shift_Ins_p.-58fs|TCF12_ENST00000452095.2_Frame_Shift_Ins_p.-224fs|TCF12_ENST00000557843.1_Frame_Shift_Ins_p.-228fs|TCF12_ENST00000560764.1_3'UTR	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12						immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		ACTTTCTTTATGCAAGGTAAGT	0.386			T	TEC	extraskeletal myxoid chondrosarcoma																																	ENST00000267811.5				Dom	yes		15	15q21	6938	T	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""			M	TEC		extraskeletal myxoid chondrosarcoma	TCF12/NR4A3(2)	0				breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36						c.(679-681)acafs		transcription factor 12																																				SO:0001589	frameshift_variant	6938				immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr15:57523450_57523451insGCAA	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.681_684dupGCAA	15.37:g.57523451_57523454dupGCAA	ENSP00000267811:p.Gln228fs					TCF12_ENST00000333725.5_Frame_Shift_Ins_p.T227fs|TCF12_ENST00000537840.1_Frame_Shift_Ins_p.Q38fs|TCF12_ENST00000343827.3_Frame_Shift_Ins_p.T57fs|TCF12_ENST00000557843.1_Frame_Shift_Ins_p.T227fs|TCF12_ENST00000560764.1_3'UTR|TCF12_ENST00000438423.2_Frame_Shift_Ins_p.T227fs|TCF12_ENST00000543579.1_Frame_Shift_Ins_p.T57fs|TCF12_ENST00000452095.2_Frame_Shift_Ins_p.T223fs	p.T227fs	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)	9	984_985	+		Colorectal(260;0.0907)	227					Q7Z3D9|Q86TC1|Q86VM2	Frame_Shift_Ins	INS	ENST00000267811.5	37	c.680_681insGCAA	CCDS10159.1																																																																																				0.386	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		52	129						52	129	---	---	---	---
TP53	7157	broad.mit.edu	37	17	7579323	7579324	+	Frame_Shift_Ins	INS	-	-	A	rs587781495		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chr17:7579323_7579324insA	ENST00000269305.4	-	4	552_553	c.363_364insT	c.(361-366)tctgtgfs	p.V122fs	TP53_ENST00000413465.2_Frame_Shift_Ins_p.V122fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.V122fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.V122fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.V122fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.V122fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	122	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		V -> L (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.G59fs*23(3)|p.S121fs*27(1)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.V122L(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGCAAGTCACAGACTTGGCTG	0.559		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	ENST00000420246.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		20	Deletion - Frameshift(9)|Whole gene deletion(8)|Deletion - In frame(2)|Substitution - Missense(1)	p.0?(8)|p.G59fs*23(3)|p.S121fs*27(1)|p.V73fs*9(1)|p.G105_T125del21(1)|p.G112_V122delGFLHSGTAKSV(1)|p.V122fs*46(1)|p.Y107fs*44(1)|p.V122L(1)|p.P13fs*18(1)|p.S33fs*23(1)	upper_aerodigestive_tract(4)|bone(4)|breast(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|stomach(1)|urinary_tract(1)|liver(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185						c.(361-366)tctgacfs	Other conserved DNA damage response genes	tumor protein p53																																				SO:0001589	frameshift_variant	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7579323_7579324insA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.364dupT	17.37:g.7579324_7579324dupA	ENSP00000269305:p.Val122fs	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_ENST00000455263.2_Frame_Shift_Ins_p.D122fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.D122fs|TP53_ENST00000269305.4_Frame_Shift_Ins_p.D122fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.D122fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.D122fs	p.D122fs	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	4	495_496	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	122		V -> L (in a sporadic cancer; somatic mutation).	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42.		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	c.363_364insT	CCDS11118.1																																																																																				0.559	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		68	33						68	33	---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153363105	153363105	+	5'UTR	DEL	G	G	-	rs587783129		TCGA-DB-A75O-01A-11D-A32B-08	TCGA-DB-A75O-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90e96e37-0f23-40b7-8277-527e8d8f0b76	b058749c-362f-4a5f-b0f7-4ab4ec256649	g.chrX:153363105delG	ENST00000303391.6	-	0	107				MECP2_ENST00000407218.1_5'UTR|MECP2_ENST00000453960.2_Frame_Shift_Del_p.A8fs	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2						adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCGGCgcggcggcggcggcgg	0.771																																						ENST00000453960.2																			0				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23						c.(16-18)gcfs		methyl CpG binding protein 2 (Rett syndrome)							4.0	5.0	5.0					X																	153363105		920	2354	3274	SO:0001623	5_prime_UTR_variant	4204				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity	g.chrX:153363105delG	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"""mental retardation, X-linked 16"", ""mental retardation, X-linked 79"", ""Rett syndrome"", ""methyl CpG binding protein 2 (Rett syndrome)"""	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.-143C>-	X.37:g.153363105delG						MECP2_ENST00000303391.6_5'UTR|MECP2_ENST00000407218.1_5'UTR	p.A8fs	NM_001110792.1	NP_001104262.1	P51608	MECP2_HUMAN			1	72	-	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		0					O15233|Q6QHH9|Q7Z384	Frame_Shift_Del	DEL	ENST00000303391.6	37	c.18delC	CCDS14741.1																																																																																				0.771	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992		2	4						2	4	---	---	---	---
