#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
NIPA1	123606	broad.mit.edu	37	15	23048861	23048861	+	Missense_Mutation	SNP	C	C	G			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr15:23048861C>G	ENST00000337435.4	-	5	982	c.958G>C	c.(958-960)Gag>Cag	p.E320Q	NIPA1_ENST00000437912.2_Missense_Mutation_p.E245Q|NIPA1_ENST00000538684.1_Missense_Mutation_p.E150Q|NIPA1_ENST00000561183.1_Missense_Mutation_p.E245Q	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	320					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		TTGTTCATCTCCCCAAGGTTG	0.478																																						uc001yvc.3																			0				endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15						c.(958-960)Gag>Cag		Homo sapiens non imprinted in Prader-Willi/Angelman syndrome 1 (NIPA1), transcript variant 1, mRNA.							85.0	82.0	83.0					15																	23048861		2203	4300	6503	SO:0001583	missense	123606				cell death	early endosome|integral to membrane|plasma membrane		g.chr15:23048861C>G	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"""spastic paraplegia 6 (autosomal dominant)"""	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.958G>C	15.37:g.23048861C>G	ENSP00000337452:p.Glu320Gln					NIPA1_uc001yvd.3_Missense_Mutation_p.E150Q|NIPA1_uc001yve.3_Missense_Mutation_p.E245Q	p.E320Q	NM_144599	NP_001135747	Q7RTP0	NIPA1_HUMAN		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)	4	983	-		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)	320					B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Missense_Mutation	SNP	ENST00000337435.4	37	c.958G>C	CCDS10011.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306024	0.40795	.	.	ENSG00000170113	ENST00000337435;ENST00000437912;ENST00000538684	D;D;T	0.90444	-2.67;-2.42;-1.1	5.74	5.74	0.90152	.	0.254797	0.44688	D	0.000437	D	0.84088	0.5395	N	0.08118	0	0.54753	D	0.999986	B	0.27791	0.189	B	0.34991	0.193	T	0.79453	-0.1797	10	0.22109	T	0.4	-21.4344	19.9111	0.97025	0.0:1.0:0.0:0.0	.	320	Q7RTP0	NIPA1_HUMAN	Q	320;245;150	ENSP00000337452:E320Q;ENSP00000393962:E245Q;ENSP00000440957:E150Q	ENSP00000337452:E320Q	E	-	1	0	NIPA1	20600302	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.933000	0.56545	2.722000	0.93159	0.591000	0.81541	GAG		0.478	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599		12	31	0	0	0	1	0	12	31				
LRRC49	54839	broad.mit.edu	37	15	71300716	71300716	+	Splice_Site	SNP	A	A	G			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr15:71300716A>G	ENST00000260382.5	+	12	1429		c.e12-1		LRRC49_ENST00000560369.1_Splice_Site|LRRC49_ENST00000443425.2_Splice_Site|LRRC49_ENST00000436542.2_Splice_Site|LRRC49_ENST00000544974.2_Splice_Site|LRRC49_ENST00000560158.2_Splice_Site|LRRC49_ENST00000560691.1_Splice_Site	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49							cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						TGGGTTTTCCAGGCCTCTAGA	0.363																																						uc010ukf.2																			0				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						c.e12-2		Homo sapiens leucine rich repeat containing 49 (LRRC49), transcript variant 1, mRNA.							69.0	72.0	71.0					15																	71300716		2199	4296	6495	SO:0001630	splice_region_variant	54839					cytoplasm|microtubule		g.chr15:71300716A>G		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1170-1A>G	15.37:g.71300716A>G						LRRC49_uc002asu.3_Splice_Site_p.G380_splice|LRRC49_uc002asx.3_Splice_Site_p.G346_splice|LRRC49_uc002asw.3_Splice_Site_p.G390_splice|LRRC49_uc002asy.3_Splice_Site_p.G96_splice|LRRC49_uc002asz.3_Splice_Site_p.G362_splice	p.G395_splice	NM_001199017	NP_001185946	Q8IUZ0	LRC49_HUMAN			12	1491	+			390					B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Splice_Site	SNP	ENST00000260382.5	37	c.1185_splice	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.010691	0.54361	.	.	ENSG00000137821	ENST00000544974;ENST00000260382;ENST00000443425;ENST00000436542	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2509	0.60052	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRC49	69087770	1.000000	0.71417	0.970000	0.41538	0.618000	0.37518	7.842000	0.86851	2.005000	0.58758	0.528000	0.53228	.		0.363	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691	Intron	4	37	0	0	0	1	0	4	37				
NYNRIN	57523	broad.mit.edu	37	14	24880401	24880401	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr14:24880401G>A	ENST00000382554.3	+	5	2852	c.2534G>A	c.(2533-2535)cGg>cAg	p.R845Q		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	845					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						AAGAAGAACCGGAGGGTGAGA	0.597											OREG0022626	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001wpf.4																			0				breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						c.(2533-2535)cGg>cAg		Homo sapiens NYN domain and retroviral integrase containing (NYNRIN), mRNA.							103.0	116.0	112.0					14																	24880401		2072	4202	6274	SO:0001583	missense	57523				DNA integration	integral to membrane	DNA binding	g.chr14:24880401G>A	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.2534G>A	14.37:g.24880401G>A	ENSP00000371994:p.Arg845Gln		OREG0022626	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	774		p.R845Q	NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN			4	2852	+			845					Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	c.2534G>A	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402356	0.83230	.	.	ENSG00000205978	ENST00000382554	T	0.40756	1.02	5.02	4.13	0.48395	Ribonuclease Zc3h12a-like (1);	.	.	.	.	T	0.37625	0.1010	N	0.04508	-0.205	0.25126	N	0.990609	D	0.71674	0.998	P	0.60473	0.875	T	0.27938	-1.0059	9	0.87932	D	0	.	10.8765	0.46915	0.0904:0.0:0.9096:0.0	.	845	Q9P2P1	NYNRI_HUMAN	Q	845	ENSP00000371994:R845Q	ENSP00000371994:R845Q	R	+	2	0	NYNRIN	23950241	0.896000	0.30565	1.000000	0.80357	0.988000	0.76386	2.251000	0.43187	1.341000	0.45600	0.467000	0.42956	CGG		0.597	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			7	141	0	0	0	1	0	7	141				
HIF1A	3091	broad.mit.edu	37	14	62203750	62203750	+	Missense_Mutation	SNP	A	A	G			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr14:62203750A>G	ENST00000337138.4	+	9	1437	c.1172A>G	c.(1171-1173)aAg>aGg	p.K391R	HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000539097.1_Missense_Mutation_p.K415R|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000394997.1_Missense_Mutation_p.K392R|HIF1A_ENST00000323441.6_Missense_Mutation_p.K391R|HIF1A_ENST00000557538.1_Missense_Mutation_p.K332R	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	391	Interaction with TSGA10. {ECO:0000250}.|N-terminal VHL recognition site.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	GACAAACTTAAGAAGGAACCT	0.393																																						uc021rua.1																			0				breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23						c.(1243-1245)aAg>aGg		Homo sapiens hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) (HIF1A), transcript variant 3, mRNA.							99.0	95.0	97.0					14																	62203750		2203	4300	6503	SO:0001583	missense	3091				cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production	cytoplasm|nucleolus|transcription factor complex	Hsp90 protein binding|histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding	g.chr14:62203750A>G	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"""Basic helix-loop-helix proteins"""	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.1172A>G	14.37:g.62203750A>G	ENSP00000338018:p.Lys391Arg					HIF1A_uc001xfq.2_Missense_Mutation_p.K391R|HIF1A_uc001xfr.2_Missense_Mutation_p.K391R|HIF1A_uc001xfs.2_Missense_Mutation_p.K392R	p.K415R	NM_001243084	NP_001230013	Q16665	HIF1A_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	8	1473	+			391			N-terminal VHL recognition site.|ODD.		C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	37	c.1244A>G	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	A	30	5.051455	0.93793	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000323441;ENST00000557538;ENST00000539097	T;T;T;T;T	0.61392	0.23;0.23;0.11;0.2;0.22	5.99	5.99	0.97316	.	0.042952	0.85682	D	0.000000	T	0.79919	0.4529	M	0.87269	2.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.83482	0.0065	10	0.87932	D	0	.	16.4947	0.84236	1.0:0.0:0.0:0.0	.	392;391;391	A8MYV6;D0VY79;Q16665	.;.;HIF1A_HUMAN	R	142;332;391;392;391;332;415	ENSP00000338018:K391R;ENSP00000378446:K392R;ENSP00000323326:K391R;ENSP00000451696:K332R;ENSP00000437955:K415R	ENSP00000323326:K391R	K	+	2	0	HIF1A	61273503	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.331000	0.96430	2.300000	0.77407	0.519000	0.50382	AAG		0.393	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		19	25	0	0	0	1	0	19	25				
CHEK2	11200	broad.mit.edu	37	22	29121246	29121246	+	Missense_Mutation	SNP	G	G	C			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr22:29121246G>C	ENST00000405598.1	-	4	620	c.429C>G	c.(427-429)caC>caG	p.H143Q	CHEK2_ENST00000404276.1_Missense_Mutation_p.H143Q|CHEK2_ENST00000328354.6_Missense_Mutation_p.H143Q|CHEK2_ENST00000382578.1_Intron|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000403642.1_Intron|CHEK2_ENST00000382566.1_Missense_Mutation_p.H143Q|CHEK2_ENST00000382580.2_Missense_Mutation_p.H186Q|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.H143Q|CHEK2_ENST00000402731.1_Missense_Mutation_p.H143Q			O96017	CHK2_HUMAN	checkpoint kinase 2	143	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						AAATCCGAAAGTGTTTCTTGC	0.373			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														uc003adt.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			0				central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(556-558)caC>caG	Direct reversal of damage;Other conserved DNA damage response genes	Homo sapiens checkpoint kinase 2 (CHEK2), transcript variant 3, mRNA.							185.0	173.0	177.0					22																	29121246		2203	4300	6503	SO:0001583	missense	11200				DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|cell cycle|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29121246G>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.429C>G	22.37:g.29121246G>C	ENSP00000386087:p.His143Gln					CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Non-coding_Transcript|CHEK2_uc010gvk.1_Non-coding_Transcript|CHEK2_uc003ads.1_5'UTR|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Missense_Mutation_p.H143Q|CHEK2_uc003adu.1_Missense_Mutation_p.H143Q|CHEK2_uc003adv.1_Missense_Mutation_p.H143Q|CHEK2_uc003adx.1_5'UTR	p.H186Q	NM_001005735	NP_001005735	O96017	CHK2_HUMAN			3	630	-			143					A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.558C>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313103	0.60414	.	.	ENSG00000183765	ENST00000348295;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	D;D;D;D;D;D;D;D;D;D	0.99186	-5.53;-5.53;-5.53;-5.53;-5.53;-5.53;-5.53;-5.53;-5.53;-5.53	5.87	3.76	0.43208	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	D	0.99278	0.9748	M	0.91818	3.245	0.58432	D	0.999995	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;0.997	D;D;D;D;D	0.97110	1.0;1.0;0.999;0.987;0.966	D	0.99521	1.0958	10	0.87932	D	0	-12.4286	9.4132	0.38505	0.2164:0.0:0.7836:0.0	.	143;143;143;143;186	O96017-7;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;CHK2_HUMAN;.	Q	143;143;143;143;143;186;143;143;174;153	ENSP00000329012:H143Q;ENSP00000372007:H143Q;ENSP00000329178:H143Q;ENSP00000385747:H143Q;ENSP00000386087:H143Q;ENSP00000372023:H186Q;ENSP00000384835:H143Q;ENSP00000397478:H143Q;ENSP00000408065:H174Q;ENSP00000381099:H153Q	ENSP00000329178:H143Q	H	-	3	2	CHEK2	27451246	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	2.113000	0.41902	0.808000	0.34231	0.585000	0.79938	CAC		0.373	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		39	5	0	0	0	1	0	39	5				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		16	37	0	0	0	1	0	16	37				
NSUN6	221078	broad.mit.edu	37	10	18840835	18840835	+	Nonsense_Mutation	SNP	C	C	A			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr10:18840835C>A	ENST00000377304.4	-	9	1406	c.988G>T	c.(988-990)Gga>Tga	p.G330*	NSUN6_ENST00000493816.1_5'Flank	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	330							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						GGTCTCTGTCCCATTCCACTA	0.428																																						uc010qcp.1																			0				endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(988-990)Gga>Tga		Homo sapiens NOP2/Sun domain family, member 6 (NSUN6), mRNA.							160.0	130.0	140.0					10																	18840835		2203	4300	6503	SO:0001587	stop_gained	221078						RNA binding|methyltransferase activity	g.chr10:18840835C>A	BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"""NOP2/Sun domain containing"""	23529	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 6"", ""NOL1/NOP2/Sun domain family, member 6"", ""ARL5B antisense RNA 1"""	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.988G>T	10.37:g.18840835C>A	ENSP00000366519:p.Gly330*						p.G330*	NM_182543	NP_872349	Q8TEA1	NSUN6_HUMAN			8	1406	-			330					B0YJ54	Nonsense_Mutation	SNP	ENST00000377304.4	37	c.988G>T	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	C	43	10.394431	0.99397	.	.	ENSG00000241058	ENST00000377304	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0537	0.97638	0.0:1.0:0.0:0.0	.	.	.	.	X	330	.	ENSP00000366519:G330X	G	-	1	0	NSUN6	18880841	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.276000	0.78559	2.758000	0.94735	0.561000	0.74099	GGA		0.428	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543		24	56	0	0	0	1	0	24	56				
DNAH9	1770	broad.mit.edu	37	17	11687720	11687720	+	Missense_Mutation	SNP	C	C	T			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr17:11687720C>T	ENST00000262442.4	+	41	7993	c.7925C>T	c.(7924-7926)gCg>gTg	p.A2642V	DNAH9_ENST00000454412.2_Missense_Mutation_p.A2642V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.A2642V(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AACTTCCCGGCGTCCCTGCAG	0.547																																						uc002gne.3																			1	Substitution - Missense(1)	p.A2642V(2)	lung(1)	NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290						c.(7924-7926)gCg>gTg		Homo sapiens dynein, axonemal, heavy chain 9 (DNAH9), transcript variant 2, mRNA.							176.0	168.0	171.0					17																	11687720		2203	4300	6503	SO:0001583	missense	1770				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:11687720C>T	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.7925C>T	17.37:g.11687720C>T	ENSP00000262442:p.Ala2642Val					DNAH9_uc010coo.3_Missense_Mutation_p.A1936V	p.A2642V	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	40	7993	+		Breast(5;0.0122)|all_epithelial(5;0.131)	2642			AAA 3 (By similarity).		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	c.7925C>T	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.356190	0.01245	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.36699	1.24;1.24	5.56	1.35	0.21983	.	0.509864	0.20467	N	0.091774	T	0.17109	0.0411	N	0.20530	0.585	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.13415	-1.0510	10	0.28530	T	0.3	.	1.0538	0.01586	0.2081:0.3493:0.2334:0.2092	.	2642	Q9NYC9	DYH9_HUMAN	V	2642;2642;1224	ENSP00000262442:A2642V;ENSP00000414874:A2642V	ENSP00000262442:A2642V	A	+	2	0	DNAH9	11628445	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.101000	0.10973	0.050000	0.15949	-0.163000	0.13421	GCG		0.547	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		76	99	0	0	0	1	0	76	99				
RET	5979	broad.mit.edu	37	10	43601916	43601916	+	Silent	SNP	C	C	T			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr10:43601916C>T	ENST00000355710.3	+	5	1192	c.960C>T	c.(958-960)ccC>ccT	p.P320P	RET_ENST00000340058.5_Silent_p.P320P	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	320					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CGCTGCTCCCCGGGGACACCT	0.657		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	uc001jal.3		1	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	"""T, Mis, N, F"""	ret proto-oncogene	yes	Hirschsprung disease	"""E, O"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	CCDC6/RET(4)|KIF5B/RET(79)	0				NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607						c.(958-960)ccC>ccT		Homo sapiens ret proto-oncogene (RET), transcript variant 2, mRNA.	Sunitinib(DB01268)						52.0	43.0	46.0					10																	43601916		2203	4299	6502	SO:0001819	synonymous_variant	5979	Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development	integral to membrane	ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity	g.chr10:43601916C>T	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.960C>T	10.37:g.43601916C>T						RET_uc001jak.1_Silent_p.P320P|RET_uc010qez.1_Silent_p.P66P	p.P320P	NM_020975	NP_066124	P07949	RET_HUMAN			4	1150	+		Ovarian(717;0.0423)	320					A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	c.960C>T	CCDS7200.1																																																																																				0.657	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		13	16	0	0	0	1	0	13	16				
TTPA	7274	broad.mit.edu	37	8	63985561	63985561	+	Missense_Mutation	SNP	C	C	A	rs368391591		TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr8:63985561C>A	ENST00000260116.4	-	2	322	c.291G>T	c.(289-291)aaG>aaT	p.K97N	TTPA_ENST00000521138.1_Intron	NM_000370.3	NP_000361.1	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	97	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)	GGTAGCCAGCCTTTAGGAGGC	0.383																																						uc003xux.2																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)	15						c.(289-291)aaG>aaT		Homo sapiens tocopherol (alpha) transfer protein (TTPA), mRNA.	Vitamin E(DB00163)	C	ASN/LYS	0,4406		0,0,2203	107.0	112.0	110.0		291	-2.0	1.0	8		110	1,8599	1.2+/-3.3	0,1,4299	no	missense	TTPA	NM_000370.3	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	97/279	63985561	1,13005	2203	4300	6503	SO:0001583	missense	7274				lipid metabolic process		transporter activity|vitamin E binding	g.chr8:63985561C>A	BC058000	CCDS6178.1	8q12.3	2007-07-18	2007-07-16			ENSG00000137561			12404	protein-coding gene	gene with protein product		600415	"""ataxia (Friedreich-like) with vitamin E deficiency"""	AVED		7719340, 7887897	Standard	NM_000370		Approved		uc003xux.2	P49638		ENST00000260116.4:c.291G>T	8.37:g.63985561C>A	ENSP00000260116:p.Lys97Asn						p.K97N	NM_000370	NP_000361	P49638	TTPA_HUMAN			1	323	-	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)	97			CRAL-TRIO.		Q71V64	Missense_Mutation	SNP	ENST00000260116.4	37	c.291G>T	CCDS6178.1	.	.	.	.	.	.	.	.	.	.	C	8.714	0.912761	0.17907	0.0	1.16E-4	ENSG00000137561	ENST00000260116	D	0.84298	-1.83	5.8	-2.02	0.07388	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.447368	0.28140	N	0.016452	T	0.59878	0.2226	N	0.08118	0	0.24078	N	0.995952	B	0.06786	0.001	B	0.10450	0.005	T	0.45977	-0.9224	10	0.18710	T	0.47	.	1.5766	0.02626	0.295:0.3029:0.0788:0.3232	.	97	P49638	TTPA_HUMAN	N	97	ENSP00000260116:K97N	ENSP00000260116:K97N	K	-	3	2	TTPA	64148115	0.242000	0.23868	0.990000	0.47175	0.983000	0.72400	-0.341000	0.07811	-0.112000	0.11979	0.643000	0.83706	AAG		0.383	TTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378460.1	NM_000370		27	35	0	0	0	1	0	27	35				
BSN	8927	broad.mit.edu	37	3	49691756	49691756	+	Silent	SNP	C	C	G			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr3:49691756C>G	ENST00000296452.4	+	5	4881	c.4767C>G	c.(4765-4767)ccC>ccG	p.P1589P		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1589					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AAACCCAGCCCACCACCCATG	0.627																																						uc003cxe.4																			0				breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106						c.(4765-4767)ccC>ccG		Homo sapiens bassoon (presynaptic cytomatrix protein) (BSN), mRNA.							72.0	66.0	68.0					3																	49691756		2203	4300	6503	SO:0001819	synonymous_variant	8927				synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding	g.chr3:49691756C>G	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.4767C>G	3.37:g.49691756C>G							p.P1589P	NM_003458	NP_003449	Q9UPA5	BSN_HUMAN		BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)	4	4881	+			1589					O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	c.4767C>G	CCDS2800.1																																																																																				0.627	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		26	50	0	0	0	1	0	26	50				
TFR2	7036	broad.mit.edu	37	7	100230955	100230955	+	Missense_Mutation	SNP	G	G	C			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr7:100230955G>C	ENST00000462107.1	-	6	910	c.623C>G	c.(622-624)cCc>cGc	p.P208R	TFR2_ENST00000544242.1_5'Flank|TFR2_ENST00000431692.1_Missense_Mutation_p.P208R|TFR2_ENST00000223051.3_Missense_Mutation_p.P208R			Q9UP52	TFR2_HUMAN	transferrin receptor 2	208					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	CAGGGTGTTGGGGTGAGCCCT	0.731																																						uc003uvv.1																			0				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						c.(622-624)cCc>cGc		Homo sapiens transferrin receptor 2 (TFR2), transcript variant 1, mRNA.							22.0	27.0	25.0					7																	100230955		2202	4299	6501	SO:0001583	missense	7036				cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity	g.chr7:100230955G>C	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.623C>G	7.37:g.100230955G>C	ENSP00000420525:p.Pro208Arg					TFR2_uc010lhc.1_5'Flank|TFR2_uc003uvu.1_Missense_Mutation_p.P37R	p.P208R	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN			4	692	-	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)		208					A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	37	c.623C>G	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191529	0.78902	.	.	ENSG00000106327	ENST00000223051;ENST00000431692;ENST00000462107	T;T;T	0.45276	0.9;0.9;0.9	5.79	5.79	0.91817	.	0.266511	0.35067	N	0.003461	T	0.27663	0.0680	N	0.08118	0	0.37959	D	0.932905	B	0.13145	0.007	B	0.12156	0.007	T	0.10894	-1.0610	10	0.41790	T	0.15	-20.5372	17.515	0.87770	0.0:0.0:1.0:0.0	.	208	Q9UP52	TFR2_HUMAN	R	208	ENSP00000223051:P208R;ENSP00000413905:P208R;ENSP00000420525:P208R	ENSP00000223051:P208R	P	-	2	0	TFR2	100068891	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.857000	0.55972	2.735000	0.93741	0.561000	0.74099	CCC		0.731	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		13	15	0	0	0	1	0	13	15				
ZNF275	10838	broad.mit.edu	37	X	152613380	152613380	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chrX:152613380G>A	ENST00000421401.3	+	4	1414	c.1237G>A	c.(1237-1239)Gtg>Atg	p.V413M	ZNF275_ENST00000370249.2_Missense_Mutation_p.V360M|ZNF275_ENST00000370251.3_3'UTR|ZNF275_ENST00000440091.1_Missense_Mutation_p.V443M			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTGTGGCCGCGTGTTCAAGAG	0.682																																						uc011myn.2																			0				endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16						c.(1048-1050)Gtg>Atg		Homo sapiens zinc finger protein 275 (ZNF275), mRNA.							5.0	6.0	6.0					X																	152613380		2035	4094	6129	SO:0001583	missense	10838					intracellular	nucleic acid binding|zinc ion binding	g.chrX:152613380G>A	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.1237G>A	X.37:g.152613380G>A	ENSP00000398977:p.Val413Met					ZNF275_uc004fhg.2_3'UTR|ZNF275_uc022cht.1_Missense_Mutation_p.V350M|ZNF275_uc022chu.1_5'Flank	p.V350M	NM_001080485	NP_001073954	A6NFS0	A6NFS0_HUMAN			1	1950	+	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		301					A6NE92	Missense_Mutation	SNP	ENST00000421401.3	37	c.1048G>A		.	.	.	.	.	.	.	.	.	.	G	10.50	1.368267	0.24771	.	.	ENSG00000063587	ENST00000421401;ENST00000440091;ENST00000370249	T;T;T	0.19105	2.17;2.17;2.17	4.59	1.79	0.24919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.221264	0.23754	N	0.044893	T	0.23572	0.0570	.	.	.	0.09310	N	1	D	0.60575	0.988	P	0.51453	0.67	T	0.11616	-1.0580	9	0.87932	D	0	-33.2403	2.9648	0.05905	0.2355:0.0:0.5448:0.2197	.	413	Q9NSD4	ZN275_HUMAN	M	413;443;360	ENSP00000398977:V413M;ENSP00000411097:V443M;ENSP00000359269:V360M	ENSP00000359269:V360M	V	+	1	0	ZNF275	152266574	0.000000	0.05858	0.527000	0.27925	0.001000	0.01503	0.636000	0.24644	0.477000	0.27464	-0.353000	0.07706	GTG		0.682	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485		5	5	0	0	0	1	0	5	5				
PDE4B	5142	broad.mit.edu	37	1	66379023	66379023	+	Missense_Mutation	SNP	C	C	T			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr1:66379023C>T	ENST00000329654.4	+	2	213	c.26C>T	c.(25-27)aCg>aTg	p.T9M	PDE4B_ENST00000371049.3_Missense_Mutation_p.T9M	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	9					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	AGTGTGATGACGGTGATGGCT	0.403																																						uc001dcn.3																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37						c.(25-27)aCg>aTg		Homo sapiens phosphodiesterase 4B, cAMP-specific (PDE4B), transcript variant d, mRNA.	Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)						146.0	134.0	138.0					1																	66379023		2203	4300	6503	SO:0001583	missense	5142				signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding	g.chr1:66379023C>T	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"""Phosphodiesterases"""	8781	protein-coding gene	gene with protein product	"""phosphodiesterase E4 dunce homolog (Drosophila)"""	600127	"""phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)"", ""phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"""	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.26C>T	1.37:g.66379023C>T	ENSP00000332116:p.Thr9Met					PDE4B_uc009war.3_5'UTR|PDE4B_uc001dco.3_Missense_Mutation_p.T9M	p.T9M	NM_001037341	NP_002591	Q07343	PDE4B_HUMAN			1	217	+			9					A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	37	c.26C>T	CCDS632.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442197	0.43326	.	.	ENSG00000184588	ENST00000329654;ENST00000341517;ENST00000371049	T;T;T	0.70282	-0.47;-0.47;-0.47	4.52	4.52	0.55395	.	0.198762	0.29653	N	0.011554	T	0.67363	0.2885	N	0.22421	0.69	0.29335	N	0.866422	D	0.76494	0.999	D	0.75020	0.985	T	0.66563	-0.5892	10	0.72032	D	0.01	.	16.3203	0.82949	0.0:1.0:0.0:0.0	.	9	Q07343	PDE4B_HUMAN	M	9	ENSP00000332116:T9M;ENSP00000342637:T9M;ENSP00000360088:T9M	ENSP00000332116:T9M	T	+	2	0	PDE4B	66151611	0.959000	0.32827	0.985000	0.45067	0.856000	0.48823	3.858000	0.55979	2.514000	0.84764	0.557000	0.71058	ACG		0.403	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		14	24	0	0	0	1	0	14	24				
FCRL2	79368	broad.mit.edu	37	1	157718364	157718364	+	Missense_Mutation	SNP	T	T	C			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr1:157718364T>C	ENST00000361516.3	-	10	1486	c.1438A>G	c.(1438-1440)Atg>Gtg	p.M480V	FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000392274.3_Intron	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	480					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GGCTGCTGCATGCTCCAGACC	0.458																																						uc001fre.2																			0				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51						c.(1438-1440)Atg>Gtg		Homo sapiens Fc receptor-like 2 (FCRL2), mRNA.							125.0	120.0	122.0					1																	157718364		2203	4300	6503	SO:0001583	missense	79368				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	SH3/SH2 adaptor activity|receptor activity	g.chr1:157718364T>C	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1438A>G	1.37:g.157718364T>C	ENSP00000355157:p.Met480Val					FCRL2_uc001frd.2_Missense_Mutation_p.M227V|FCRL2_uc010phz.1_Intron|FCRL2_uc009wsp.2_Intron	p.M480V	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.24)		9	1497	-	all_hematologic(112;0.0378)		480					A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	c.1438A>G	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	T	0.038	-1.297830	0.01364	.	.	ENSG00000132704	ENST00000361516	T	0.18016	2.24	3.67	1.17	0.20885	.	11.288600	0.00166	U	0.000006	T	0.02156	0.0067	N	0.04508	-0.205	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.34030	-0.9845	10	0.27082	T	0.32	.	4.3318	0.11067	0.2008:0.0:0.2087:0.5905	.	480;227	Q96LA5;Q96LA5-2	FCRL2_HUMAN;.	V	480	ENSP00000355157:M480V	ENSP00000355157:M480V	M	-	1	0	FCRL2	155984988	0.020000	0.18652	0.009000	0.14445	0.009000	0.06853	2.380000	0.44327	0.102000	0.17638	-0.336000	0.08194	ATG		0.458	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		47	31	0	0	0	1	0	47	31				
CUX1	1523	broad.mit.edu	37	7	101877481	101877481	+	Missense_Mutation	SNP	G	G	T			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr7:101877481G>T	ENST00000292535.7	+	22	3621	c.3583G>T	c.(3583-3585)Gtg>Ttg	p.V1195L	CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.V1206L|CUX1_ENST00000549414.2_Missense_Mutation_p.V1173L|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.V1037L|CUX1_ENST00000550008.2_Missense_Mutation_p.V1139L|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000546411.2_Missense_Mutation_p.V1093L|CUX1_ENST00000292538.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1195					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CCCCAACAATGTGGAGAAGCT	0.577																																						uc003uys.4																			0				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						c.(3616-3618)Gtg>Ttg		Homo sapiens cut-like homeobox 1 (CUX1), transcript variant 4, mRNA.							70.0	62.0	64.0					7																	101877481		2203	4300	6503	SO:0001583	missense	1523				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:101877481G>T	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.3583G>T	7.37:g.101877481G>T	ENSP00000292535:p.Val1195Leu					CUX1_uc003uyw.3_Intron|CUX1_uc003uyv.3_Intron|CUX1_uc003uyt.3_Intron|CUX1_uc003uyu.3_Intron|CUX1_uc011kkn.2_Intron|CUX1_uc003uyx.4_Missense_Mutation_p.V1195L	p.V1206L	NM_001202543	NP_001189472	P39880	CUX1_HUMAN			21	3743	+			1195					B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	37	c.3616G>T	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349823	0.95830	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.64438	-0.06;-0.05;-0.1;-0.1;-0.07;-0.09	5.32	5.32	0.75619	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.74473	0.3721	L	0.43152	1.355	0.80722	D	1	D;D	0.67145	0.967;0.996	D;D	0.77557	0.97;0.99	T	0.76561	-0.2914	10	0.72032	D	0.01	-23.15	19.0082	0.92861	0.0:0.0:1.0:0.0	.	1195;1206	P39880;P39880-3	CUX1_HUMAN;.	L	1206;1195;1173;1139;1093;1037	ENSP00000353401:V1206L;ENSP00000292535:V1195L;ENSP00000446630:V1173L;ENSP00000447373:V1139L;ENSP00000450125:V1093L;ENSP00000451558:V1037L	ENSP00000292535:V1195L	V	+	1	0	CUX1	101664201	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.864000	0.99589	2.486000	0.83907	0.655000	0.94253	GTG		0.577	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		30	42	0	0	0	1	0	30	42				
PLEKHN1	84069	broad.mit.edu	37	1	902110	902113	+	Frame_Shift_Del	DEL	GCCT	GCCT	-			TCGA-KS-A4IB-01A-11D-A257-08	TCGA-KS-A4IB-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b3724d56-88c0-4852-9cea-315377062ea9	c02af1ba-df99-42e4-a70e-71765a149770	g.chr1:902110_902113delGCCT	ENST00000379409.2	+	2	140_143	c.110_113delGCCT	c.(109-114)ggcctgfs	p.GL37fs	PLEKHN1_ENST00000379407.3_Frame_Shift_Del_p.GL37fs|PLEKHN1_ENST00000379410.3_Frame_Shift_Del_p.GL37fs			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	37										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		ATGTCGGCCGGCCTGCCGGGCCCC	0.74																																						uc001ace.3																			0				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9						c.(109-114)ggcctgfs		Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	84069							g.chr1:902110_902113delGCCT	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.110_113delGCCT	1.37:g.902110_902113delGCCT	ENSP00000368719:p.Gly37fs					PLEKHN1_uc001acd.3_Frame_Shift_Del_p.G37fs|PLEKHN1_uc001acf.3_Frame_Shift_Del_p.G37fs	p.G37fs	NM_032129	NP_115505	Q494U1	PKHN1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)	1	145_148	+	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)	37					Q494U2|Q5SV98|Q9H0M7	Frame_Shift_Del	DEL	ENST00000379409.2	37	c.110_113delGCCT																																																																																					0.740	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		5	1						5	1	---	---	---	---
