#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
GJB3	2707	broad.mit.edu	37	1	35250842	35250842	+	Missense_Mutation	SNP	G	G	A	rs200055020		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:35250842G>A	ENST00000373366.2	+	2	1094	c.479G>A	c.(478-480)cGc>cAc	p.R160H	RP1-34M23.5_ENST00000542839.1_RNA|GJB3_ENST00000373362.3_Missense_Mutation_p.R160H	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	160					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)	p.R160H(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AATATGCCGCGCCTGGTGCAG	0.552													g|||	1	0.000199681	0.0	0.0014	5008	,	,		20625	0.0		0.0	False		,,,				2504	0.0					uc001bxx.2																			1	Substitution - Missense(1)		endometrium(1)		0						c.(478-480)CGC>CAC		connexin 31			HIS/ARG,HIS/ARG	2,4404	2.1+/-5.4	0,2,2201	152.0	162.0	159.0		479,479	5.1	1.0	1		159	4,8596	4.3+/-15.6	0,4,4296	yes	missense,missense	GJB3	NM_001005752.1,NM_024009.2	29,29	0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461	possibly-damaging,possibly-damaging	160/271,160/271	35250842	6,13000	2203	4300	6503	SO:0001583	missense	2707				cell communication	connexon complex|integral to membrane	gap junction channel activity	g.chr1:35250842G>A	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"""Ion channels / Gap junction proteins (connexins)"""	4285	protein-coding gene	gene with protein product	"""connexin 31"""	603324	"""gap junction protein, beta 3, 31kD (connexin 31)"", ""gap junction protein, beta 3, 31kDa (connexin 31)"", ""erythrokeratodermia variabilis"""	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.479G>A	1.37:g.35250842G>A	ENSP00000362464:p.Arg160His					GJB3_uc001bxy.2_Missense_Mutation_p.R160H|GJB3_uc001bxz.3_Missense_Mutation_p.R160H|uc010ohs.1_RNA	p.R160H	NM_024009	NP_076872	O75712	CXB3_HUMAN			2	1094	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)	160			Extracellular (Potential).		B2R790|Q2TAZ8	Missense_Mutation	SNP	ENST00000373366.2	37	c.479G>A	CCDS384.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	g	10.40	1.340688	0.24339	4.54E-4	4.65E-4	ENSG00000188910	ENST00000373366;ENST00000373362;ENST00000543647	D;D	0.95656	-3.77;-3.77	5.07	5.07	0.68467	Gap junction protein, cysteine-rich domain (1);	0.109633	0.64402	N	0.000017	D	0.92176	0.7519	M	0.61703	1.905	0.47476	D	0.999435	P	0.38300	0.626	B	0.23574	0.047	D	0.91616	0.5307	10	0.36615	T	0.2	.	13.7745	0.63046	0.0:0.154:0.846:0.0	.	160	O75712	CXB3_HUMAN	H	160;160;144	ENSP00000362464:R160H;ENSP00000362460:R160H	ENSP00000362460:R160H	R	+	2	0	GJB3	35023429	1.000000	0.71417	0.997000	0.53966	0.019000	0.09904	7.821000	0.86641	2.368000	0.80403	0.556000	0.70494	CGC		0.552	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009	
EPHA10	284656	broad.mit.edu	37	1	38227109	38227109	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:38227109G>A	ENST00000373048.4	-	3	817	c.818C>T	c.(817-819)gCg>gTg	p.A273V	EPHA10_ENST00000427468.2_Missense_Mutation_p.A273V|EPHA10_ENST00000319637.6_Missense_Mutation_p.A273V	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	273					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CTGGAATCCCGCGCTGCAGCT	0.677																																						uc009vvi.2																			0				breast(4)|stomach(3)|lung(1)	8						c.(817-819)GCG>GTG		EPH receptor A10 isofom 3							36.0	39.0	38.0					1																	38227109		2163	4186	6349	SO:0001583	missense	284656					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity	g.chr1:38227109G>A	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.818C>T	1.37:g.38227109G>A	ENSP00000362139:p.Ala273Val					EPHA10_uc001cbw.3_Missense_Mutation_p.A273V	p.A273V	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN			3	904	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)	273			Extracellular (Potential).		A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	c.818C>T	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964911	0.74131	.	.	ENSG00000183317	ENST00000427468;ENST00000373048;ENST00000319637	D;D;T	0.97529	-4.42;-4.42;4.28	4.23	4.23	0.50019	Tyrosine-protein kinase, receptor class V, conserved site (1);	0.000000	0.41500	D	0.000875	D	0.97266	0.9106	M	0.77486	2.375	0.80722	D	1	D;D	0.69078	0.996;0.997	P;P	0.50659	0.644;0.647	D	0.97787	1.0236	10	0.66056	D	0.02	.	16.1124	0.81273	0.0:0.0:1.0:0.0	.	273;273	Q5JZY3;Q5JZY3-2	EPHAA_HUMAN;.	V	273	ENSP00000397746:A273V;ENSP00000362139:A273V;ENSP00000316395:A273V	ENSP00000316395:A273V	A	-	2	0	EPHA10	37999696	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.352000	0.66028	2.328000	0.79073	0.551000	0.68910	GCG		0.677	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
LRRIQ3	127255	broad.mit.edu	37	1	74507363	74507363	+	Nonsense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:74507363G>A	ENST00000395089.1	-	6	1251	c.1252C>T	c.(1252-1254)Cga>Tga	p.R418*	LRRIQ3_ENST00000354431.4_Nonsense_Mutation_p.R418*			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	418										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CTAAATGTTCGGAGTTTCATA	0.363																																						uc001dfy.3																			0				ovary(2)	2						c.(1252-1254)CGA>TGA		leucine-rich repeats and IQ motif containing 3							139.0	126.0	130.0					1																	74507363		1843	4079	5922	SO:0001587	stop_gained	127255							g.chr1:74507363G>A	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1252C>T	1.37:g.74507363G>A	ENSP00000378524:p.Arg418*					LRRIQ3_uc001dfz.3_Intron	p.R418*	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN			7	1444	-			418					A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Nonsense_Mutation	SNP	ENST00000395089.1	37	c.1252C>T	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.704285	0.68615	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	.	.	.	5.77	-4.33	0.03677	.	1.149140	0.06593	N	0.752394	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	9.5583	0.39353	0.0:0.2722:0.1921:0.5357	.	.	.	.	X	418	.	ENSP00000346414:R418X	R	-	1	2	LRRIQ3	74279951	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.209000	0.09358	-0.389000	0.07786	0.585000	0.79938	CGA		0.363	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
Unknown	0	broad.mit.edu	37	1	144615288	144615288	+	IGR	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:144615288C>T								RP11-640M9.2 (9397 upstream) : NBPF9 (196455 downstream)																							CCTGGCCAACCGACAGAAGAA	0.448																																						uc009wig.1																			0					0						c.(160-162)CGA>TGA		hypothetical protein LOC400818																																				SO:0001628	intergenic_variant	400818					cytoplasm		g.chr1:144615288C>T																													1.37:g.144615288C>T						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_5'UTR|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_5'UTR|NBPF9_uc010oyg.1_Missense_Mutation_p.P53L|NBPF9_uc009wii.1_5'UTR|NBPF9_uc009wif.1_RNA|C1orf152_uc001elf.3_5'Flank	p.R54*	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN			4	236	+			54						Nonsense_Mutation	SNP		37	c.160C>T																																																																																				0	0.448								
LOC728989	728989	broad.mit.edu	37	1	146494510	146494510	+	IGR	SNP	T	T	C	rs11585592|rs34958799	byFrequency	TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:146494510T>C								RP4-704D21.2 (19333 upstream) : RNVU1-8 (56784 downstream)																							TGCCAGGCAGTGCAGGGATGT	0.557													.|||	1678	0.335064	0.3328	0.2723	5008	,	,		20743	0.2758		0.4732	False		,,,				2504	0.3016					uc001epd.2																			0					0						c.(487-489)GCA>GCG		SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;																																				SO:0001628	intergenic_variant	728989							g.chr1:146494510T>C																													1.37:g.146494510T>C							p.A163A	NR_024442						4	563	-									Silent	SNP		37	c.489A>G																																																																																				0	0.557								
ILDR2	387597	broad.mit.edu	37	1	166904584	166904584	+	Missense_Mutation	SNP	A	A	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr1:166904584A>T	ENST00000271417.3	-	6	889	c.834T>A	c.(832-834)caT>caA	p.H278Q	ILDR2_ENST00000529071.1_Missense_Mutation_p.H259Q|ILDR2_ENST00000528703.1_Intron|ILDR2_ENST00000529387.1_Intron|ILDR2_ENST00000525740.1_Intron|ILDR2_ENST00000469934.2_Missense_Mutation_p.H278Q|ILDR2_ENST00000526687.1_Intron	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	278					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						AGGGAGGTGGATGCGGCTTGT	0.617																																						uc001gdx.1																			0				ovary(1)	1						c.(832-834)CAT>CAA		immunoglobulin-like domain containing receptor							95.0	87.0	90.0					1																	166904584		2203	4300	6503	SO:0001583	missense	387597					integral to membrane		g.chr1:166904584A>T	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"""LISCH-like"""		"""chromosome 1 open reading frame 32"""	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.834T>A	1.37:g.166904584A>T	ENSP00000271417:p.His278Gln						p.H278Q	NM_199351	NP_955383	Q71H61	ILDR2_HUMAN			6	890	-			278			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000271417.3	37	c.834T>A	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	A	11.86	1.765428	0.31228	.	.	ENSG00000143195	ENST00000271417;ENST00000469934;ENST00000529071	T;T;T	0.54479	0.57;0.58;0.57	5.67	2.12	0.27331	.	0.243574	0.42420	D	0.000712	T	0.16514	0.0397	L	0.36672	1.1	0.80722	D	1	B	0.15473	0.013	B	0.10450	0.005	T	0.08106	-1.0738	10	0.20519	T	0.43	-3.9366	2.4395	0.04490	0.5297:0.0:0.2582:0.2121	.	278	Q71H61	ILDR2_HUMAN	Q	278;278;259	ENSP00000271417:H278Q;ENSP00000437008:H278Q;ENSP00000436882:H259Q	ENSP00000271417:H278Q	H	-	3	2	ILDR2	165171208	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.614000	0.24314	0.949000	0.37715	0.459000	0.35465	CAT		0.617	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351	
MPP7	143098	broad.mit.edu	37	10	28345469	28345469	+	Silent	SNP	T	T	C			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr10:28345469T>C	ENST00000375732.1	-	16	1750	c.1491A>G	c.(1489-1491)acA>acG	p.T497T	MPP7_ENST00000540098.1_Silent_p.T497T|MPP7_ENST00000337532.5_Silent_p.T497T|MPP7_ENST00000375719.3_Silent_p.T497T			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	497	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						CATTTTTTCTTGTTTCTCTCA	0.403																																						uc001iua.1																			0				ovary(1)	1						c.(1489-1491)ACA>ACG		palmitoylated membrane protein 7							202.0	195.0	197.0					10																	28345469		2203	4300	6503	SO:0001819	synonymous_variant	143098				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity	g.chr10:28345469T>C	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.1491A>G	10.37:g.28345469T>C						MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Silent_p.T497T|MPP7_uc009xla.2_Silent_p.T497T|MPP7_uc010qdv.1_RNA	p.T497T	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN			18	1895	-			497			Guanylate kinase-like.		B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Silent	SNP	ENST00000375732.1	37	c.1491A>G	CCDS7158.1																																																																																				0.403	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496	
OGDHL	55753	broad.mit.edu	37	10	50943387	50943387	+	Missense_Mutation	SNP	G	G	A	rs534879619		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr10:50943387G>A	ENST00000374103.4	-	23	3005	c.2920C>T	c.(2920-2922)Cgg>Tgg	p.R974W	OGDHL_ENST00000419399.1_Missense_Mutation_p.R917W|OGDHL_ENST00000490844.1_5'UTR|OGDHL_ENST00000432695.1_Missense_Mutation_p.R765W	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	974					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						GCTGGGTCCCGGCCAACATAC	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		11056	0.001		0.0	False		,,,				2504	0.0					uc001jie.2																			0				pancreas(1)	1						c.(2920-2922)CGG>TGG		oxoglutarate dehydrogenase-like isoform a							72.0	75.0	74.0					10																	50943387		2203	4300	6503	SO:0001583	missense	55753				glycolysis	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding	g.chr10:50943387G>A	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2920C>T	10.37:g.50943387G>A	ENSP00000363216:p.Arg974Trp					OGDHL_uc009xog.2_Missense_Mutation_p.R1001W|OGDHL_uc010qgt.1_Missense_Mutation_p.R917W|OGDHL_uc010qgu.1_Missense_Mutation_p.R765W	p.R974W	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN			23	3062	-			974					A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	c.2920C>T	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.757346	0.89843	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;T	0.12879	2.64;2.64;2.64	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	H	0.98466	4.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76334	-0.2997	10	0.87932	D	0	.	18.7651	0.91869	0.0:0.0:1.0:0.0	.	917;765;974	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	W	974;917;765	ENSP00000363216:R974W;ENSP00000401356:R917W;ENSP00000390240:R765W	ENSP00000363216:R974W	R	-	1	2	OGDHL	50613393	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	7.195000	0.77798	2.515000	0.84797	0.655000	0.94253	CGG		0.622	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
A1CF	29974	broad.mit.edu	37	10	52596064	52596064	+	Missense_Mutation	SNP	C	C	T	rs148254279		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr10:52596064C>T	ENST00000373993.1	-	4	418	c.374G>A	c.(373-375)cGc>cAc	p.R125H	A1CF_ENST00000373995.3_Missense_Mutation_p.R133H|A1CF_ENST00000395489.2_Missense_Mutation_p.R118H|A1CF_ENST00000395495.1_Missense_Mutation_p.R125H|A1CF_ENST00000373997.3_Missense_Mutation_p.R125H|A1CF_ENST00000374001.2_Missense_Mutation_p.R125H|A1CF_ENST00000282641.2_Missense_Mutation_p.R125H			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	125	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CCCTAAGAGGCGCCCATTTCT	0.438																																						uc001jjj.2																			0				central_nervous_system(1)	1						c.(373-375)CGC>CAC		apobec-1 complementation factor isoform 2		C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	53.0	54.0	54.0		374,398,398,374,374,398	5.9	1.0	10	dbSNP_134	54	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	125/587,133/603,133/595,125/587,125/595,133/595	52596064	1,13005	2203	4300	6503	SO:0001583	missense	29974				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding	g.chr10:52596064C>T	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.374G>A	10.37:g.52596064C>T	ENSP00000363105:p.Arg125His					A1CF_uc010qhn.1_Missense_Mutation_p.R133H|A1CF_uc001jji.2_Missense_Mutation_p.R125H|A1CF_uc001jjh.2_Missense_Mutation_p.R133H|A1CF_uc010qho.1_Missense_Mutation_p.R133H|A1CF_uc009xov.2_Missense_Mutation_p.R125H	p.R125H	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN			6	562	-			125			RRM 1.		A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	37	c.374G>A	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116059	0.77323	2.27E-4	0.0	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;3.0;0.6;3.0;3.0;3.0	5.94	5.94	0.96194	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.72070	0.3415	M	0.66939	2.045	0.80722	D	1	D;P;D;P	0.89917	0.972;0.784;1.0;0.937	B;P;D;B	0.87578	0.445;0.458;0.998;0.248	T	0.72017	-0.4417	10	0.59425	D	0.04	-5.8377	17.8605	0.88779	0.0:1.0:0.0:0.0	.	118;125;125;133	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	H	125;125;125;133;125;125;108;118;125	ENSP00000363113:R125H;ENSP00000363105:R125H;ENSP00000363109:R125H;ENSP00000363107:R133H;ENSP00000282641:R125H;ENSP00000378873:R125H;ENSP00000378868:R118H;ENSP00000397953:R125H	ENSP00000282641:R125H	R	-	2	0	A1CF	52266070	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.731000	0.84895	2.814000	0.96858	0.563000	0.77884	CGC		0.438	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
CNNM1	26507	broad.mit.edu	37	10	101147663	101147663	+	Silent	SNP	C	C	T	rs532479735		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr10:101147663C>T	ENST00000356713.4	+	8	2716	c.2427C>T	c.(2425-2427)gaC>gaT	p.D809D	CNNM1_ENST00000446890.1_Silent_p.D738D|CNNM1_ENST00000370534.4_Silent_p.D465D|CNNM1_ENST00000370528.3_Silent_p.D738D	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	809					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.D444D(1)|p.D809D(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CCTTCACAGACGGGGACTCCA	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20228	0.0		0.0	False		,,,				2504	0.0					uc001kpp.3																			2	Substitution - coding silent(2)		endometrium(2)		0						c.(2425-2427)GAC>GAT		cyclin M1							63.0	56.0	59.0					10																	101147663		2203	4300	6503	SO:0001819	synonymous_variant	26507				ion transport	integral to membrane|plasma membrane		g.chr10:101147663C>T	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2427C>T	10.37:g.101147663C>T						CNNM1_uc010qpi.1_Silent_p.D830D|CNNM1_uc009xwf.2_Silent_p.D809D|CNNM1_uc009xwg.2_Silent_p.D209D	p.D809D	NM_020348	NP_065081	Q9NRU3	CNNM1_HUMAN		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)	8	2716	+		Colorectal(252;0.234)	809					Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	c.2427C>T	CCDS7478.2																																																																																				0.602	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
DCHS1	8642	broad.mit.edu	37	11	6654846	6654846	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr11:6654846C>T	ENST00000299441.3	-	5	2663	c.2252G>A	c.(2251-2253)cGg>cAg	p.R751Q	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	751	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGAATTGGCCCGTCTGGCCAA	0.547																																						uc001mem.1																			0				ovary(3)|large_intestine(1)|pancreas(1)	5						c.(2251-2253)CGG>CAG		dachsous 1 precursor							26.0	23.0	24.0					11																	6654846		2201	4295	6496	SO:0001583	missense	8642				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr11:6654846C>T	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2252G>A	11.37:g.6654846C>T	ENSP00000299441:p.Arg751Gln						p.R751Q	NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	5	2662	-		Medulloblastoma(188;0.00263)|all_neural(188;0.026)	751			Cadherin 7.|Extracellular (Potential).		O15098	Missense_Mutation	SNP	ENST00000299441.3	37	c.2252G>A	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511033	0.64522	.	.	ENSG00000166341	ENST00000299441	T	0.50813	0.73	5.37	2.27	0.28462	Cadherin (4);Cadherin-like (1);	0.358932	0.20396	N	0.093146	T	0.48874	0.1524	L	0.33137	0.985	0.29084	N	0.882504	D	0.76494	0.999	D	0.63877	0.919	T	0.37865	-0.9687	10	0.46703	T	0.11	.	6.4333	0.21809	0.0:0.5971:0.0:0.4029	.	751	Q96JQ0	PCD16_HUMAN	Q	751	ENSP00000299441:R751Q	ENSP00000299441:R751Q	R	-	2	0	DCHS1	6611422	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.936000	0.48971	0.650000	0.30769	0.561000	0.74099	CGG		0.547	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
OR4C6	219432	broad.mit.edu	37	11	55432767	55432767	+	Missense_Mutation	SNP	T	T	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr11:55432767T>A	ENST00000314259.3	+	1	154	c.125T>A	c.(124-126)cTt>cAt	p.L42H		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						GAAAATCTACTTATTGTGGTA	0.393																																						uc001nht.3																			0				skin(2)	2						c.(124-126)CTT>CAT		olfactory receptor, family 4, subfamily C,							257.0	231.0	240.0					11																	55432767		2200	4296	6496	SO:0001583	missense	219432				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55432767T>A	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.125T>A	11.37:g.55432767T>A	ENSP00000324769:p.Leu42His					OR4C6_uc010rik.1_Missense_Mutation_p.L42H	p.L42H	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN			3	390	+			42			Helical; Name=1; (Potential).		B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	c.125T>A	CCDS31506.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.709911	0.48517	.	.	ENSG00000181903	ENST00000314259	T	0.02890	4.12	3.83	3.83	0.44106	GPCR, rhodopsin-like superfamily (1);	0.243616	0.21022	N	0.081484	T	0.18882	0.0453	H	0.96015	3.755	0.09310	N	1	D	0.58620	0.983	P	0.58577	0.841	T	0.18745	-1.0327	10	0.87932	D	0	.	11.4815	0.50328	0.0:0.0:0.0:1.0	.	42	Q8NH72	OR4C6_HUMAN	H	42	ENSP00000324769:L42H	ENSP00000324769:L42H	L	+	2	0	OR4C6	55189343	0.000000	0.05858	0.122000	0.21767	0.008000	0.06430	-0.219000	0.09228	1.387000	0.46486	0.444000	0.29173	CTT		0.393	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
TMEM109	79073	broad.mit.edu	37	11	60687272	60687272	+	Missense_Mutation	SNP	G	G	A	rs139328208		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr11:60687272G>A	ENST00000227525.3	+	2	510	c.107G>A	c.(106-108)cGt>cAt	p.R36H	RP11-881M11.4_ENST00000543907.1_RNA|TMEM109_ENST00000536171.1_Missense_Mutation_p.R36H	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	36					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						GCCCAGTCCCGTCGAGACTTT	0.547													A|||	1	0.000199681	0.0	0.0014	5008	,	,		21054	0.0		0.0	False		,,,				2504	0.0					uc001nqg.2																			0					0						c.(106-108)CGT>CAT		transmembrane protein 109 precursor		A	HIS/ARG	0,4406		0,0,2203	157.0	133.0	141.0		107	2.2	0.0	11	dbSNP_134	141	2,8596	819.1+/-406.8	0,2,4297	no	missense	TMEM109	NM_024092.2	29	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	36/244	60687272	2,13002	2203	4299	6502	SO:0001583	missense	79073					integral to membrane|nuclear outer membrane|sarcoplasmic reticulum membrane		g.chr11:60687272G>A		CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.107G>A	11.37:g.60687272G>A	ENSP00000227525:p.Arg36His					TMEM109_uc001nqh.2_Missense_Mutation_p.R36H	p.R36H	NM_024092	NP_076997	Q9BVC6	TM109_HUMAN			2	485	+			36						Missense_Mutation	SNP	ENST00000227525.3	37	c.107G>A	CCDS7996.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.059388	0.00386	0.0	2.33E-4	ENSG00000110108	ENST00000227525;ENST00000446886;ENST00000536171	.	.	.	4.62	2.19	0.27852	.	0.253989	0.32533	N	0.005974	T	0.07638	0.0192	N	0.00500	-1.43	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33033	-0.9884	9	0.23302	T	0.38	-0.4052	6.4044	0.21656	0.5797:0.3359:0.0844:0.0	.	36	Q9BVC6	TM109_HUMAN	H	36	.	ENSP00000227525:R36H	R	+	2	0	TMEM109	60443848	0.073000	0.21202	0.027000	0.17364	0.023000	0.10783	0.994000	0.29693	0.017000	0.15025	-0.360000	0.07572	CGT		0.547	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092	
NXF1	10482	broad.mit.edu	37	11	62561731	62561731	+	Splice_Site	SNP	T	T	C			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr11:62561731T>C	ENST00000532297.1	-	20	2388	c.1759A>G	c.(1759-1761)Aag>Gag	p.K587E	TMEM223_ENST00000525631.1_5'Flank|NXF1_ENST00000294172.2_Splice_Site_p.K587E|TMEM223_ENST00000307366.7_5'Flank|TMEM223_ENST00000527073.1_5'Flank|NXF1_ENST00000531709.2_3'UTR|NXF1_ENST00000533048.1_5'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	587	TAP-C. {ECO:0000255|PROSITE- ProRule:PRU00611}.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGCACTCACTTCTGGGACCAC	0.517																																						uc001nvf.1																			0				skin(3)	3						c.(1759-1761)AAG>GAG		nuclear RNA export factor 1 isoform 1							68.0	60.0	63.0					11																	62561731		2201	4299	6500	SO:0001630	splice_region_variant	10482				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding	g.chr11:62561731T>C	AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"""tip associating protein"""	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.1760+1A>G	11.37:g.62561731T>C						TMEM223_uc001nve.2_5'Flank|NXF1_uc001nvg.1_3'UTR|NXF1_uc009yog.1_3'UTR	p.K587E	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN			19	1895	-			587			TAP-C.		B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	c.1759A>G	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.523964	0.85600	.	.	ENSG00000162231	ENST00000294172;ENST00000532297	T;T	0.49139	0.79;0.79	5.21	4.04	0.47022	TAP, C-terminal (3);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.66356	0.2781	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65038	-0.6265	10	0.21014	T	0.42	-21.3044	10.507	0.44839	0.0:0.0:0.1632:0.8368	.	587	Q9UBU9	NXF1_HUMAN	E	587	ENSP00000294172:K587E;ENSP00000436679:K587E	ENSP00000294172:K587E	K	-	1	0	NXF1	62318307	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.697000	0.84279	0.894000	0.36317	0.459000	0.35465	AAG		0.517	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362	Missense_Mutation
MAP4K2	5871	broad.mit.edu	37	11	64559447	64559448	+	Frame_Shift_Ins	INS	-	-	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr11:64559447_64559448insG	ENST00000294066.2	-	27	2116_2117	c.2025_2026insC	c.(2023-2028)ggctgcfs	p.C676fs	MAP4K2_ENST00000377350.3_Frame_Shift_Ins_p.C668fs	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	676	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						AGGACGCGGCAGCCGGGCCCCT	0.708																																						uc001obh.2																			0				ovary(1)|pancreas(1)	2						c.(2023-2028)GGCTGCfs		mitogen-activated protein kinase kinase kinase				67,4105		2,63,2021						3.2	1.0			12	137,7985		3,131,3927	no	frameshift	MAP4K2	NM_004579.3		5,194,5948	A1A1,A1R,RR		1.6868,1.6059,1.6593				204,12090				SO:0001589	frameshift_variant	5871				activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity	g.chr11:64559447_64559448insG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.2026dupC	11.37:g.64559448_64559448dupG	ENSP00000294066:p.Cys676fs					MAP4K2_uc001obg.2_RNA|MAP4K2_uc001obi.2_Frame_Shift_Ins_p.G667fs	p.G675fs	NM_004579	NP_004570	Q12851	M4K2_HUMAN			27	2117_2118	-			675_676			CNH.		Q86VU3	Frame_Shift_Ins	INS	ENST00000294066.2	37	c.2025_2026insC	CCDS8082.1																																																																																				0.708	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579	
Unknown	0	broad.mit.edu	37	12	92116	92116	+	IGR	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr12:92116C>T								AC215219.1 (18794 upstream) : AC026369.1 (54935 downstream)																							CAGCGCCAGGCAGTGGTGCAG	0.597																																						uc010sdi.1																			0											c.(193-195)TGC>TAC		SubName: Full=DEAD/H box polypeptide 11 like 11;																																				SO:0001628	intergenic_variant	0							g.chr12:92116C>T																													12.37:g.92116C>T						uc010sdj.1_RNA	p.C65Y							2	222	-									Missense_Mutation	SNP		37	c.194G>A																																																																																				0	0.597								
Unknown	0	broad.mit.edu	37	12	92127	92127	+	IGR	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr12:92127C>T								AC215219.1 (18805 upstream) : AC026369.1 (54924 downstream)																							AGTGGTGCAGCTGCCTGTCAG	0.582																																						uc010sdi.1																			0											c.(181-183)CAG>CAA		SubName: Full=DEAD/H box polypeptide 11 like 11;																																				SO:0001628	intergenic_variant	0							g.chr12:92127C>T																													12.37:g.92127C>T						uc010sdj.1_RNA	p.Q61Q							2	211	-									Silent	SNP		37	c.183G>A																																																																																				0	0.582								
SLCO1B7	338821	broad.mit.edu	37	12	21229466	21229466	+	Nonsense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr12:21229466C>T	ENST00000421593.2	+	12	1687	c.1687C>T	c.(1687-1689)Cga>Tga	p.R563*	SLCO1B3_ENST00000553473.1_Nonsense_Mutation_p.R671*|LST3_ENST00000381541.3_Nonsense_Mutation_p.R610*|LST3_ENST00000540229.1_Nonsense_Mutation_p.R671*|SLCO1B7_ENST00000554957.1_Nonsense_Mutation_p.R610*|RP11-125O5.2_ENST00000590779.1_Silent_p.H63H	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	563						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						CTGTGGAGCACGAGGGGCTTG	0.358																																						uc010sil.1																			0				large_intestine(2)|ovary(1)|skin(1)	4						c.(2011-2013)CGA>TGA		SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;							175.0	185.0	182.0					12																	21229466		2203	4300	6503	SO:0001587	stop_gained	28234				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity	g.chr12:21229466C>T	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.1687C>T	12.37:g.21229466C>T	ENSP00000394168:p.Arg563*					LST-3TM12_uc010sim.1_Nonsense_Mutation_p.R610*|LST-3TM12_uc010sin.1_Nonsense_Mutation_p.R563*	p.R671*			Q9NPD5	SO1B3_HUMAN			15	2076	+	Esophageal squamous(101;0.149)		Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					Q71QF0	Nonsense_Mutation	SNP	ENST00000421593.2	37	c.2011C>T	CCDS44843.1	.	.	.	.	.	.	.	.	.	.	.	19.91	3.914658	0.72983	.	.	ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754;ENSG00000205754;ENSG00000205754	ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957;ENST00000421593;ENST00000545916	.	.	.	2.4	1.32	0.21799	.	0.513584	0.20032	N	0.100694	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.5507	0.04748	0.2889:0.5365:0.0:0.1746	.	.	.	.	X	671;610;671;610;563;72	.	ENSP00000370952:R610X	R	+	1	2	SLCO1B3;SLCO1B7;RP11-545J16.1	21120733	0.001000	0.12720	0.003000	0.11579	0.513000	0.34164	0.863000	0.27913	1.322000	0.45245	0.205000	0.17691	CGA		0.358	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
STAC3	246329	broad.mit.edu	37	12	57642900	57642900	+	Silent	SNP	G	G	A	rs148939626		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr12:57642900G>A	ENST00000332782.2	-	3	459	c.258C>T	c.(256-258)aaC>aaT	p.N86N	STAC3_ENST00000554578.1_Silent_p.N47N|STAC3_ENST00000546246.2_Intron	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	86					intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						GGGGCTTATCGTTGACCAGCT	0.507																																						uc001snp.2																			0				ovary(2)|skin(1)	3						c.(256-258)AAC>AAT		SH3 and cysteine rich domain 3		G		0,4406		0,0,2203	95.0	96.0	95.0		258	-1.0	1.0	12	dbSNP_134	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	STAC3	NM_145064.1		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		86/365	57642900	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	246329				intracellular signal transduction		identical protein binding|metal ion binding	g.chr12:57642900G>A	AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.258C>T	12.37:g.57642900G>A						STAC3_uc009zpl.2_Intron|STAC3_uc001snq.2_Silent_p.N47N|STAC3_uc010srm.1_Intron	p.N86N	NM_145064	NP_659501	Q96MF2	STAC3_HUMAN			3	453	-			86					B4DUK9|Q96HU5	Silent	SNP	ENST00000332782.2	37	c.258C>T	CCDS8936.1																																																																																				0.507	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064	
SACS	26278	broad.mit.edu	37	13	23908788	23908788	+	Missense_Mutation	SNP	G	G	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr13:23908788G>T	ENST00000382292.3	-	9	9500	c.9227C>A	c.(9226-9228)aCt>aAt	p.T3076N	SACS_ENST00000382298.3_Missense_Mutation_p.T3076N|SACS_ENST00000402364.1_Missense_Mutation_p.T2326N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3076					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AAGATTAGCAGTTTCATCACA	0.358																																						uc001uon.2																			0				ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12						c.(9226-9228)ACT>AAT		sacsin							93.0	88.0	89.0					13																	23908788		2203	4300	6503	SO:0001583	missense	26278				cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding	g.chr13:23908788G>T	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.9227C>A	13.37:g.23908788G>T	ENSP00000371729:p.Thr3076Asn					SACS_uc001uoo.2_Missense_Mutation_p.T2929N|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	p.T3076N	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)	10	9816	-		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)	3076					O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	c.9227C>A	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012046	0.75046	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88201	-2.2;-2.35;-2.2	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.92580	0.7643	L	0.43152	1.355	0.51482	D	0.999929	D	0.89917	1.0	D	0.85130	0.997	D	0.91724	0.5391	10	0.42905	T	0.14	.	19.7024	0.96060	0.0:0.0:1.0:0.0	.	3076	Q9NZJ4	SACS_HUMAN	N	3076;2326;3076	ENSP00000371729:T3076N;ENSP00000385844:T2326N;ENSP00000371735:T3076N	ENSP00000371729:T3076N	T	-	2	0	SACS	22806788	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.653000	0.90120	0.555000	0.69702	ACT		0.358	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SPTB	6710	broad.mit.edu	37	14	65270332	65270332	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr14:65270332C>T	ENST00000389721.5	-	3	499	c.467G>A	c.(466-468)cGc>cAc	p.R156H	SPTB_ENST00000556626.1_Missense_Mutation_p.R156H|SPTB_ENST00000542895.1_Missense_Mutation_p.R156H|SPTB_ENST00000389720.3_Missense_Mutation_p.R156H|SPTB_ENST00000389722.3_Missense_Mutation_p.R156H	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	156	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CACCTGGAAGCGGAGGATGAT	0.572																																						uc001xht.2																			0				ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11						c.(466-468)CGC>CAC		spectrin beta isoform b							87.0	85.0	85.0					14																	65270332		2203	4300	6503	SO:0001583	missense	6710				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton	g.chr14:65270332C>T		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.467G>A	14.37:g.65270332C>T	ENSP00000374371:p.Arg156His					SPTB_uc001xhr.2_Missense_Mutation_p.R156H|SPTB_uc001xhs.2_Missense_Mutation_p.R156H|SPTB_uc001xhu.2_Missense_Mutation_p.R156H	p.R156H	NM_000347	NP_000338	P11277	SPTB1_HUMAN		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)	3	521	-		all_lung(585;4.15e-09)	156			CH 1.|Actin-binding.		Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	c.467G>A	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	34	5.334579	0.95758	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27	5.38	5.38	0.77491	Calponin homology domain (5);	0.108970	0.64402	D	0.000004	T	0.71736	0.3375	L	0.45470	1.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73560	-0.3944	10	0.87932	D	0	.	18.2717	0.90070	0.0:1.0:0.0:0.0	.	156;160	P11277;Q59FP5	SPTB1_HUMAN;.	H	160;156;156;156;156;156	ENSP00000374372:R156H;ENSP00000451752:R156H;ENSP00000374371:R156H;ENSP00000443882:R156H;ENSP00000374370:R156H	ENSP00000374370:R156H	R	-	2	0	SPTB	64340085	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	7.755000	0.85180	2.677000	0.91161	0.563000	0.77884	CGC		0.572	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
WDR72	256764	broad.mit.edu	37	15	53992060	53992060	+	Missense_Mutation	SNP	A	A	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr15:53992060A>T	ENST00000396328.1	-	13	1891	c.1652T>A	c.(1651-1653)cTg>cAg	p.L551Q	WDR72_ENST00000559418.1_Missense_Mutation_p.L561Q|WDR72_ENST00000557913.1_Missense_Mutation_p.L548Q|WDR72_ENST00000360509.5_Missense_Mutation_p.L551Q	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	551										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CCGGGCATGCAGGAGGCAACT	0.463																																						uc002acj.2																			0				lung(1)|skin(1)	2						c.(1651-1653)CTG>CAG		WD repeat domain 72							124.0	130.0	128.0					15																	53992060		2194	4293	6487	SO:0001583	missense	256764							g.chr15:53992060A>T	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1652T>A	15.37:g.53992060A>T	ENSP00000379619:p.Leu551Gln					WDR72_uc010bfi.1_Missense_Mutation_p.L551Q	p.L551Q	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN		all cancers(107;0.0511)	13	1694	-			551			WD 7.		Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	c.1652T>A	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974179	0.74246	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.01295	5.04;5.04	5.72	5.72	0.89469	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.377447	0.25391	N	0.031017	T	0.07369	0.0186	M	0.71581	2.175	0.38366	D	0.944733	D	0.64830	0.994	D	0.64321	0.924	T	0.03969	-1.0988	10	0.62326	D	0.03	.	15.4793	0.75511	1.0:0.0:0.0:0.0	.	551	Q3MJ13	WDR72_HUMAN	Q	551	ENSP00000379619:L551Q;ENSP00000353699:L551Q	ENSP00000353699:L551Q	L	-	2	0	WDR72	51779352	1.000000	0.71417	0.212000	0.23672	0.856000	0.48823	8.138000	0.89613	2.311000	0.77944	0.533000	0.62120	CTG		0.463	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
MEF2A	4205	broad.mit.edu	37	15	100230497	100230497	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr15:100230497G>A	ENST00000557785.1	+	8	1071	c.722G>A	c.(721-723)gGt>gAt	p.G241D	MEF2A_ENST00000558812.1_Missense_Mutation_p.G173D|MEF2A_ENST00000453228.2_Missense_Mutation_p.G241D|MEF2A_ENST00000338042.6_Missense_Mutation_p.G241D|MEF2A_ENST00000354410.5_Missense_Mutation_p.G243D|MEF2A_ENST00000449277.2_Missense_Mutation_p.G173D|MEF2A_ENST00000557942.1_Missense_Mutation_p.G241D	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	243					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GGAGCTACTGGTGCAAATAGC	0.413																																						uc010urw.1																			0				ovary(1)	1						c.(727-729)GGT>GAT		myocyte enhancer factor 2A isoform 1							48.0	45.0	46.0					15																	100230497		1828	4098	5926	SO:0001583	missense	4205				apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development	nuclear chromatin|nucleoplasm	activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding	g.chr15:100230497G>A		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.722G>A	15.37:g.100230497G>A	ENSP00000453441:p.Gly241Asp					MEF2A_uc010urv.1_Missense_Mutation_p.G173D|MEF2A_uc010bos.2_Missense_Mutation_p.G241D|MEF2A_uc002bvf.2_Missense_Mutation_p.G243D|MEF2A_uc002bve.2_Missense_Mutation_p.G241D|MEF2A_uc002bvg.2_Missense_Mutation_p.G241D|MEF2A_uc002bvi.2_Missense_Mutation_p.G241D|MEF2A_uc010bot.2_Missense_Mutation_p.G173D	p.G243D	NM_005587	NP_005578	Q02078	MEF2A_HUMAN	OV - Ovarian serous cystadenocarcinoma(32;0.00085)		7	1087	+	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		243					B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	37	c.728G>A	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	G	33	5.239064	0.95240	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T;T	0.60672	0.19;0.17;0.2;1.19	5.55	5.55	0.83447	.	0.043128	0.85682	D	0.000000	T	0.66005	0.2746	L	0.46157	1.445	0.48288	D	0.999626	P;D;D;P;P;D	0.61697	0.647;0.983;0.964;0.911;0.76;0.99	B;P;P;P;P;P	0.53689	0.371;0.662;0.581;0.506;0.575;0.732	T	0.67898	-0.5551	10	0.72032	D	0.01	-17.6563	19.8622	0.96787	0.0:0.0:1.0:0.0	.	243;173;162;241;243;241	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	D	241;243;241;173	ENSP00000404110:G241D;ENSP00000346389:G243D;ENSP00000337202:G241D;ENSP00000399460:G173D	ENSP00000337202:G241D	G	+	2	0	MEF2A	98048020	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.571000	0.82399	2.769000	0.95229	0.650000	0.86243	GGT		0.413	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
DNM1P47	100216544	broad.mit.edu	37	15	102292797	102292797	+	RNA	SNP	C	C	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr15:102292797C>G	ENST00000561463.1	+	0	843									DNM1 pseudogene 47									p.P129A(2)									GAGCTGCTGTCCAACCTGCAC	0.597																																						uc010usj.1																			2	Substitution - Missense(2)		urinary_tract(1)|lung(1)								c.(385-387)CCA>GCA		RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																																						0							g.chr15:102292797C>G	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102292797C>G						uc002bxo.2_RNA|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank	p.P129A							4	444	+									Missense_Mutation	SNP	ENST00000561463.1	37	c.385C>G																																																																																					0.597	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149	
CACNA1H	8912	broad.mit.edu	37	16	1255218	1255218	+	Nonsense_Mutation	SNP	C	C	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr16:1255218C>A	ENST00000348261.5	+	11	2804	c.2556C>A	c.(2554-2556)taC>taA	p.Y852*	CACNA1H_ENST00000358590.4_Nonsense_Mutation_p.Y852*|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Nonsense_Mutation_p.Y852*	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	852					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CTCTGGGCTACATCCGGAACC	0.597																																						uc002cks.2																			0				breast(2)	2						c.(2554-2556)TAC>TAA		calcium channel, voltage-dependent, T type,	Flunarizine(DB04841)|Mibefradil(DB01388)						81.0	85.0	84.0					16																	1255218		2087	4211	6298	SO:0001587	stop_gained	8912				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity	g.chr16:1255218C>A	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2556C>A	16.37:g.1255218C>A	ENSP00000334198:p.Tyr852*					CACNA1H_uc002ckt.2_Nonsense_Mutation_p.Y852*	p.Y852*	NM_021098	NP_066921	O95180	CAC1H_HUMAN			11	2804	+		Hepatocellular(780;0.00369)	852			II.|Cytoplasmic (Potential).		B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Nonsense_Mutation	SNP	ENST00000348261.5	37	c.2556C>A	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	39	7.299440	0.98196	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	.	.	.	3.93	2.97	0.34412	.	0.072567	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6295	0.45527	0.0:0.905:0.0:0.095	.	.	.	.	X	852	.	ENSP00000334198:Y852X	Y	+	3	2	CACNA1H	1195219	1.000000	0.71417	0.909000	0.35828	0.022000	0.10575	1.890000	0.39728	0.866000	0.35629	0.655000	0.94253	TAC		0.597	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
MAPK8IP3	23162	broad.mit.edu	37	16	1816093	1816093	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr16:1816093G>A	ENST00000250894.4	+	21	2733	c.2576G>A	c.(2575-2577)cGg>cAg	p.R859Q	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.R853Q	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	859					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)	p.R859Q(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						AACGTGCCGCGGAGCAACTGC	0.662																																						uc002cmk.2																			1	Substitution - Missense(1)		prostate(1)	breast(2)|central_nervous_system(1)	3						c.(2575-2577)CGG>CAG		mitogen-activated protein kinase 8 interacting							33.0	44.0	40.0					16																	1816093		2114	4226	6340	SO:0001583	missense	23162				vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding	g.chr16:1816093G>A	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2576G>A	16.37:g.1816093G>A	ENSP00000250894:p.Arg859Gln					MAPK8IP3_uc002cml.2_Missense_Mutation_p.R853Q|MAPK8IP3_uc010uvl.1_Missense_Mutation_p.R860Q	p.R859Q	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN			21	2696	+			859					A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	37	c.2576G>A	CCDS10442.2	.	.	.	.	.	.	.	.	.	.	G	10.06	1.246218	0.22796	.	.	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.29917	1.55;1.55	4.99	3.04	0.35103	.	0.114453	0.64402	D	0.000009	T	0.35595	0.0937	L	0.60455	1.87	0.58432	D	0.999993	P;P;P	0.52463	0.569;0.953;0.853	B;P;P	0.50352	0.129;0.638;0.447	T	0.05818	-1.0862	10	0.23302	T	0.38	-14.7528	10.4188	0.44338	0.1604:0.0:0.8396:0.0	.	860;853;859	B7ZMF3;E9PFH7;Q9UPT6	.;.;JIP3_HUMAN	Q	859;853	ENSP00000250894:R859Q;ENSP00000348290:R853Q	ENSP00000250894:R859Q	R	+	2	0	MAPK8IP3	1756094	1.000000	0.71417	0.113000	0.21522	0.079000	0.17450	5.146000	0.64845	0.528000	0.28580	0.561000	0.74099	CGG		0.662	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
SCNN1G	6340	broad.mit.edu	37	16	23200784	23200784	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr16:23200784G>A	ENST00000300061.2	+	3	553	c.410G>A	c.(409-411)cGc>cAc	p.R137H		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	137					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TCCCGGAAGCGCCGAGAGGCG	0.577																																						uc002dlm.1																			0				ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6						c.(409-411)CGC>CAC		sodium channel, nonvoltage-gated 1, gamma	Amiloride(DB00594)|Triamterene(DB00384)						85.0	95.0	91.0					16																	23200784		2197	4300	6497	SO:0001583	missense	6340				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding	g.chr16:23200784G>A	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10602	protein-coding gene	gene with protein product		600761	"""sodium channel, nonvoltage-gated 1, gamma"", ""sodium channel, non-voltage-gated 1, gamma"""			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.410G>A	16.37:g.23200784G>A	ENSP00000300061:p.Arg137His						p.R137H	NM_001039	NP_001030	P51170	SCNNG_HUMAN		GBM - Glioblastoma multiforme(48;0.0366)	3	549	+			137			Extracellular (By similarity).		P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	37	c.410G>A	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.823806	0.50739	.	.	ENSG00000166828	ENST00000300061	T	0.64438	-0.1	5.75	4.77	0.60923	.	0.138562	0.34386	N	0.004016	T	0.51686	0.1689	N	0.08118	0	0.28219	N	0.926625	D	0.57899	0.981	P	0.54401	0.751	T	0.48725	-0.9010	10	0.36615	T	0.2	-11.5624	10.7804	0.46374	0.0923:0.0:0.9077:0.0	.	137	P51170	SCNNG_HUMAN	H	137	ENSP00000300061:R137H	ENSP00000300061:R137H	R	+	2	0	SCNN1G	23108285	0.996000	0.38824	0.285000	0.24819	0.128000	0.20619	2.615000	0.46368	1.355000	0.45865	0.511000	0.50034	CGC		0.577	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
IL4R	3566	broad.mit.edu	37	16	27357789	27357789	+	Splice_Site	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr16:27357789G>A	ENST00000395762.2	+	6	622	c.363G>A	c.(361-363)gtG>gtA	p.V121V	IL4R_ENST00000543915.2_Splice_Site_p.V121V|IL4R_ENST00000170630.2_Splice_Site_p.V121V|IL4R_ENST00000449195.1_Splice_Site_p.V121V|IL4R_ENST00000380922.3_Splice_Site_p.V106V	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	121					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CTCCCGCAGTGAAACCCAGGG	0.567																																						uc002don.2																			0				ovary(1)|skin(1)	2						c.(361-363)GTG>GTA		interleukin 4 receptor alpha chain isoform a							65.0	59.0	61.0					16																	27357789		2197	4300	6497	SO:0001630	splice_region_variant	3566				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity	g.chr16:27357789G>A	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.362-1G>A	16.37:g.27357789G>A						IL4R_uc002dom.2_Silent_p.V121V|IL4R_uc002dop.3_Silent_p.V106V|IL4R_uc010bxy.2_Silent_p.V121V|IL4R_uc002doo.2_5'UTR	p.V121V	NM_000418	NP_000409	P24394	IL4RA_HUMAN			6	605	+			121			Extracellular (Potential).		B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	c.363G>A	CCDS10629.1																																																																																				0.567	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		Silent
DNAH9	1770	broad.mit.edu	37	17	11684359	11684359	+	Missense_Mutation	SNP	G	G	A	rs377663702		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:11684359G>A	ENST00000262442.4	+	39	7654	c.7586G>A	c.(7585-7587)gGc>gAc	p.G2529D	DNAH9_ENST00000454412.2_Missense_Mutation_p.G2529D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2529	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)			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)		AAGAAGGCTGGCAGAAACTAT	0.542																																						uc002gne.2																			0				skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20						c.(7585-7587)GGC>GAC		dynein, axonemal, heavy chain 9 isoform 2		G	ASP/GLY	0,4406		0,0,2203	42.0	38.0	40.0		7586	5.1	0.9	17		40	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH9	NM_001372.3	94	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	2529/4487	11684359	1,13005	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.chr17:11684359G>A	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.7586G>A	17.37:g.11684359G>A	ENSP00000262442:p.Gly2529Asp					DNAH9_uc010coo.2_Missense_Mutation_p.G1823D	p.G2529D	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	39	7654	+		Breast(5;0.0122)|all_epithelial(5;0.131)	2529			AAA 3 (By similarity).		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	c.7586G>A	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.775825	0.90195	0.0	1.16E-4	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.55760	0.5;0.5	5.08	5.08	0.68730	ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000001	D	0.82467	0.5043	H	0.96861	3.895	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.88722	0.3230	10	0.87932	D	0	.	18.8287	0.92128	0.0:0.0:1.0:0.0	.	2529	Q9NYC9	DYH9_HUMAN	D	2529;2529;1111	ENSP00000262442:G2529D;ENSP00000414874:G2529D	ENSP00000262442:G2529D	G	+	2	0	DNAH9	11625084	1.000000	0.71417	0.932000	0.37286	0.886000	0.51366	9.767000	0.98960	2.526000	0.85167	0.637000	0.83480	GGC		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CDRT15	146822	broad.mit.edu	37	17	14140072	14140072	+	Nonsense_Mutation	SNP	G	G	A	rs147270904	byFrequency	TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:14140072G>A	ENST00000420162.2	-	1	94	c.79C>T	c.(79-81)Cga>Tga	p.R27*	CDRT15_ENST00000431716.2_Missense_Mutation_p.P2L	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	27								p.R27*(1)		endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGCCTTCTTCGGCATCGTCGG	0.597													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20399	0.0		0.0	False		,,,				2504	0.0					uc010vvu.1																			1	Substitution - Nonsense(1)		lung(1)		0						c.(79-81)CGA>TGA		CMT1A duplicated region transcript 15		G	stop/ARG	6,4400	11.4+/-27.6	0,6,2197	46.0	43.0	44.0		79	-1.0	0.0	17	dbSNP_134	44	0,8596		0,0,4298	no	stop-gained	CDRT15	NM_001007530.1		0,6,6495	AA,AG,GG		0.0,0.1362,0.0461		27/189	14140072	6,12996	2203	4298	6501	SO:0001587	stop_gained	146822							g.chr17:14140072G>A	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.79C>T	17.37:g.14140072G>A	ENSP00000402355:p.Arg27*					CDRT15_uc010coq.2_RNA	p.R27*	NM_001007530	NP_001007531	Q96T59	CDRTF_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)	1	79	-			27					B2RUU5	Nonsense_Mutation	SNP	ENST00000420162.2	37	c.79C>T	CCDS32569.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.91|11.91	1.781075|1.781075	0.31502|0.31502	0.001362|0.001362	0.0|0.0	ENSG00000223510|ENSG00000223510	ENST00000431716|ENST00000420162	.|.	.|.	.|.	0.675|0.675	-0.987|-0.987	0.10249|0.10249	.|.	.|.	.|.	.|.	.|.	T|.	0.09291|.	0.0229|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34279|.	-0.9835|.	4|.	0.87932|0.02654	D|T	0|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	L|X	2|27	.|.	ENSP00000399575:P2L|ENSP00000402355:R27X	P|R	-|-	2|1	0|2	CDRT15|CDRT15	14080797|14080797	0.958000|0.958000	0.32768|0.32768	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.277000|-0.277000	0.08502|0.08502	-0.311000|-0.311000	0.08754|0.08754	0.289000|0.289000	0.19496|0.19496	CCG|CGA		0.597	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
CCL3	6348	broad.mit.edu	37	17	34416095	34416095	+	Nonsense_Mutation	SNP	G	G	A	rs5029409	byFrequency	TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:34416095G>A	ENST00000225245.5	-	3	284	c.202C>T	c.(202-204)Cga>Tga	p.R68*	AC069363.1_ENST00000441575.1_RNA|AC069363.1_ENST00000592728.1_RNA|AC069363.1_ENST00000590992.1_RNA	NM_002983.2	NP_002974.1	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	68		Involved in GAG binding.			astrocyte cell migration (GO:0043615)|behavior (GO:0007610)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|eosinophil degranulation (GO:0043308)|exocytosis (GO:0006887)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoclast differentiation (GO:0045671)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell migration (GO:0030335)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of tumor necrosis factor production (GO:0032760)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|response to toxic substance (GO:0009636)|signaling (GO:0023052)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)	calcium-dependent protein kinase C activity (GO:0004698)|CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			breast(2)|lung(3)|urinary_tract(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGCCGGCTTCGCTTGGTTAGG	0.597																																						uc002hkv.2																			0					0						c.(202-204)CGA>TGA		chemokine (C-C motif) ligand 3							105.0	106.0	106.0					17																	34416095		2203	4300	6503	SO:0001587	stop_gained	6348				cell-cell signaling|cellular calcium ion homeostasis|cellular component movement|cytoskeleton organization|exocytosis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|regulation of viral genome replication	extracellular space|soluble fraction	chemoattractant activity|chemokine activity|signal transducer activity	g.chr17:34416095G>A	M23178	CCDS11307.1	17q12	2014-05-06	2002-08-22	2002-08-23	ENSG00000006075	ENSG00000277632		"""Chemokine ligands"", ""Endogenous ligands"""	10627	protein-coding gene	gene with protein product		182283	"""small inducible cytokine A3 (homologous to mouse Mip-1a)"""	SCYA3			Standard	NM_002983		Approved	G0S19-1, LD78ALPHA, MIP-1-alpha	uc002hkv.3	P10147	OTTHUMG00000188413	ENST00000225245.5:c.202C>T	17.37:g.34416095G>A	ENSP00000225245:p.Arg68*						p.R68*	NM_002983	NP_002974	P10147	CCL3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	3	304	-		Ovarian(249;0.17)	68	R->A: Strongly reduces heparin binding.			Involved in GAG binding.		Nonsense_Mutation	SNP	ENST00000225245.5	37	c.202C>T	CCDS11307.1	.	.	.	.	.	.	.	.	.	.	.	16.54	3.152017	0.57151	.	.	ENSG00000006075	ENST00000225245	.	.	.	5.82	5.82	0.92795	.	0.754623	0.12169	N	0.493209	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	10.2218	0.43201	0.0:0.0:0.1669:0.8331	.	.	.	.	X	68	.	ENSP00000225245:R68X	R	-	1	2	CCL3	31440208	0.786000	0.28738	0.627000	0.29227	0.088000	0.18126	2.174000	0.42482	1.032000	0.39892	-0.264000	0.10439	CGA		0.597	CCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256581.1	NM_002983	
KRT19	3880	broad.mit.edu	37	17	39680449	39680449	+	Missense_Mutation	SNP	G	G	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:39680449G>T	ENST00000361566.3	-	5	954	c.894C>A	c.(892-894)gaC>gaA	p.D298E	KRT15_ENST00000254043.3_5'Flank|KRT15_ENST00000393976.2_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	298	Coil 2.|Necessary for interaction with PNN.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				TGCGCCGCAGGTCAGTAACCT	0.577																																						uc010wfs.1																			0				ovary(2)|lung(2)|breast(1)	5						c.(1381-1383)GAC>GAA		junction plakoglobin							49.0	51.0	51.0					17																	39680449		2203	4300	6503	SO:0001583	missense	3728				adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity	g.chr17:39680449G>T		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.894C>A	17.37:g.39680449G>T	ENSP00000355124:p.Asp298Glu					KRT15_uc002hxb.1_5'Flank|uc002hxc.1_5'Flank|KRT19_uc002hxd.3_Missense_Mutation_p.D298E	p.D461E	NM_021991	NP_068831	P14923	PLAK_HUMAN	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)	8	1391	-		Breast(137;0.000162)	Error:Variant_position_missing_in_P14923_after_alignment					B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	37	c.1383C>A	CCDS11399.1	.	.	.	.	.	.	.	.	.	.	G	1.625	-0.520432	0.04171	.	.	ENSG00000171345	ENST00000361566	D	0.86366	-2.11	5.26	0.562	0.17290	Prefoldin (1);Filament (1);	0.267510	0.26421	N	0.024473	T	0.61627	0.2362	N	0.02169	-0.655	0.33548	D	0.595791	B;B	0.27316	0.0;0.175	B;B	0.33339	0.002;0.162	T	0.61426	-0.7065	10	0.02654	T	1	.	4.8409	0.13489	0.0695:0.1983:0.2123:0.5199	.	461;298	B4DE59;P08727	.;K1C19_HUMAN	E	298	ENSP00000355124:D298E	ENSP00000355124:D298E	D	-	3	2	KRT19	36933975	0.000000	0.05858	0.991000	0.47740	0.396000	0.30629	-2.440000	0.01016	0.186000	0.20125	0.563000	0.77884	GAC		0.577	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276	
RP11-156P1.2	0	broad.mit.edu	37	17	45127410	45127410	+	IGR	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:45127410C>T	ENST00000571841.1	+	0	889				RP11-156P1.3_ENST00000575173.1_RNA|LRRC37A17P_ENST00000570478.1_RNA																							CTGATGCTCGCAAACAGGCCT	0.473																																						uc010wkj.1																			0											c.(607-609)GCA>GTA		SubName: Full=Putative uncharacterized protein LRRC37A3;																																				SO:0001628	intergenic_variant	0							g.chr17:45127410C>T																													17.37:g.45127410C>T						uc010wkl.1_RNA	p.A203V							2	962	+									Missense_Mutation	SNP	ENST00000571841.1	37	c.608C>T																																																																																					0.473	RP11-156P1.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000440447.1		
IGF2BP1	10642	broad.mit.edu	37	17	47115648	47115648	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:47115648C>T	ENST00000290341.3	+	6	854	c.520C>T	c.(520-522)Cgg>Tgg	p.R174W	RNU6-826P_ENST00000516827.1_RNA|IGF2BP1_ENST00000431824.2_Intron	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	174					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTTTGGCTCTCGGGGTCAGCC	0.652																																					Esophageal Squamous(198;1041 2123 8248 37119 38268)	uc002iom.2																			0				kidney(1)	1						c.(520-522)CGG>TGG		insulin-like growth factor 2 mRNA binding							32.0	38.0	36.0					17																	47115648		2203	4300	6503	SO:0001583	missense	10642				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity	g.chr17:47115648C>T	AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"""RNA binding motif (RRM) containing"""	28866	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 1"""	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.520C>T	17.37:g.47115648C>T	ENSP00000290341:p.Arg174Trp					IGF2BP1_uc010dbj.2_Intron	p.R174W	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN			6	854	+			174					C9JT33	Missense_Mutation	SNP	ENST00000290341.3	37	c.520C>T	CCDS11543.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757789	0.89843	.	.	ENSG00000159217	ENST00000290341	T	0.22945	1.93	5.55	4.56	0.56223	.	0.000000	0.64402	D	0.000001	T	0.39835	0.1093	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	P	0.55391	0.775	T	0.30031	-0.9992	10	0.72032	D	0.01	-22.2604	13.0106	0.58729	0.2936:0.7064:0.0:0.0	.	174	Q9NZI8	IF2B1_HUMAN	W	174	ENSP00000290341:R174W	ENSP00000290341:R174W	R	+	1	2	IGF2BP1	44470647	0.926000	0.31397	0.982000	0.44146	0.988000	0.76386	1.985000	0.40668	1.280000	0.44463	0.655000	0.94253	CGG		0.652	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546	
SOX9	6662	broad.mit.edu	37	17	70117782	70117782	+	Missense_Mutation	SNP	T	T	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr17:70117782T>G	ENST00000245479.2	+	1	622	c.250T>G	c.(250-252)Tac>Gac	p.Y84D		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	84					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			GCTCAAAGGCTACGACTGGAC	0.637																																					Pancreas(42;83 1041 2320 35205 39456)	uc002jiw.2																			0					0						c.(250-252)TAC>GAC		transcription factor SOX9							51.0	36.0	41.0					17																	70117782		2202	4299	6501	SO:0001583	missense	6662				cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	g.chr17:70117782T>G	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"""SRY (sex determining region Y)-boxes"""	11204	protein-coding gene	gene with protein product		608160	"""campomelic dysplasia, autosomal sex-reversal"""	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.250T>G	17.37:g.70117782T>G	ENSP00000245479:p.Tyr84Asp					uc002jiv.2_5'Flank	p.Y84D	NM_000346	NP_000337	P48436	SOX9_HUMAN	STAD - Stomach adenocarcinoma(260;0.119)		1	622	+		Colorectal(1115;0.245)	84					Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	37	c.250T>G	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.553471	0.86127	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	D	0.93076	-3.16	4.39	4.39	0.52855	.	0.000000	0.85682	U	0.000000	D	0.97238	0.9097	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98080	1.0403	10	0.87932	D	0	.	13.6215	0.62140	0.0:0.0:0.0:1.0	.	84	P48436	SOX9_HUMAN	D	84	ENSP00000245479:Y84D	ENSP00000245479:Y84D	Y	+	1	0	SOX9	67629377	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.808000	0.86044	1.625000	0.50366	0.402000	0.26972	TAC		0.637	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346	
EPB41L3	23136	broad.mit.edu	37	18	5406824	5406824	+	Silent	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr18:5406824G>A	ENST00000341928.2	-	16	2641	c.2301C>T	c.(2299-2301)gcC>gcT	p.A767A	EPB41L3_ENST00000400111.3_Silent_p.A586A|EPB41L3_ENST00000544123.1_Silent_p.A598A|EPB41L3_ENST00000542146.1_Silent_p.A39A|EPB41L3_ENST00000427684.2_Silent_p.A39A|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000342933.3_Silent_p.A767A|EPB41L3_ENST00000540638.2_Silent_p.A586A	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	767	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CCTGCCTGGCGGCCAGTCGCA	0.527																																						uc002kmt.1																			0				ovary(5)	5						c.(2299-2301)GCC>GCT		erythrocyte membrane protein band 4.1-like 3							128.0	106.0	114.0					18																	5406824		2203	4300	6503	SO:0001819	synonymous_variant	23136				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity	g.chr18:5406824G>A	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2301C>T	18.37:g.5406824G>A						EPB41L3_uc010wzh.1_Silent_p.A598A|EPB41L3_uc002kmu.1_Silent_p.A586A|EPB41L3_uc010dkq.1_Silent_p.A477A|EPB41L3_uc002kms.1_Silent_p.A39A|EPB41L3_uc010wze.1_Silent_p.A39A|EPB41L3_uc010wzf.1_Silent_p.A39A|EPB41L3_uc010wzg.1_Silent_p.A39A|EPB41L3_uc010dkr.2_Silent_p.A159A	p.A767A	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN			16	2387	-			767			Spectrin--actin-binding (Potential).		B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	37	c.2301C>T	CCDS11838.1																																																																																				0.527	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
SERPINB2	5055	broad.mit.edu	37	18	61569672	61569672	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr18:61569672G>A	ENST00000299502.4	+	7	793	c.713G>A	c.(712-714)cGt>cAt	p.R238H	SERPINB2_ENST00000457692.1_Missense_Mutation_p.R238H|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	238					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ATGTACTTGCGTGAAAAGCTA	0.363																																						uc010xeu.1																			0				lung(1)|skin(1)	2						c.(712-714)CGT>CAT		serine (or cysteine) proteinase inhibitor, clade	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)						116.0	104.0	108.0					18																	61569672		2203	4300	6503	SO:0001583	missense	5055				anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity	g.chr18:61569672G>A	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.713G>A	18.37:g.61569672G>A	ENSP00000299502:p.Arg238His					SERPINB2_uc002ljo.2_Missense_Mutation_p.R238H|SERPINB2_uc010dqh.2_Missense_Mutation_p.R168H|SERPINB2_uc002ljp.1_Missense_Mutation_p.R43H|SERPINB2_uc002ljq.1_Missense_Mutation_p.R43H	p.R238H	NM_001143818	NP_001137290	P05120	PAI2_HUMAN			8	1046	+		Esophageal squamous(42;0.131)	238					Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	c.713G>A	CCDS11989.1	.	.	.	.	.	.	.	.	.	.	G	6.437	0.448841	0.12223	.	.	ENSG00000197632	ENST00000299502;ENST00000457692	D;D	0.84660	-1.88;-1.88	5.4	-2.15	0.07102	Serpin domain (3);	0.914875	0.09431	N	0.803012	T	0.71863	0.3390	N	0.20610	0.595	0.23602	N	0.997317	B;B	0.11235	0.004;0.004	B;B	0.10450	0.005;0.003	T	0.54289	-0.8316	10	0.30854	T	0.27	.	8.8716	0.35320	0.3909:0.1083:0.5009:0.0	.	238;238	B2R7Y0;P05120	.;PAI2_HUMAN	H	238	ENSP00000299502:R238H;ENSP00000401645:R238H	ENSP00000299502:R238H	R	+	2	0	SERPINB2	59720652	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.538000	0.00938	-0.560000	0.06102	-0.355000	0.07637	CGT		0.363	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
CACNA1A	773	broad.mit.edu	37	19	13410023	13410023	+	Silent	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:13410023C>T	ENST00000360228.5	-	19	2423	c.2424G>A	c.(2422-2424)acG>acA	p.T808T	CACNA1A_ENST00000573710.2_Silent_p.T809T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	809					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAGGTGCCGCGTGTAGGCAG	0.642																																						uc010dze.2																			0				large_intestine(2)	2						c.(2425-2427)ACG>ACA		calcium channel, alpha 1A subunit isoform 3	Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)						45.0	53.0	50.0					19																	13410023		2031	4156	6187	SO:0001819	synonymous_variant	773				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding	g.chr19:13410023C>T	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.2424G>A	19.37:g.13410023C>T						CACNA1A_uc010dzc.2_Silent_p.T334T|CACNA1A_uc002mwy.3_Silent_p.T808T|CACNA1A_uc010xne.1_Silent_p.T337T	p.T809T	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		19	2663	-			809			Cytoplasmic (Potential).		J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	c.2427G>A	CCDS45998.1																																																																																				0.642	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
FCGBP	8857	broad.mit.edu	37	19	40368357	40368357	+	Missense_Mutation	SNP	C	C	T	rs367948062		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:40368357C>T	ENST00000221347.6	-	28	12998	c.12991G>A	c.(12991-12993)Gcc>Acc	p.A4331T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4331						extracellular vesicular exosome (GO:0070062)		p.A4331T(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCTGGCAGGCGGCCACGTAG	0.647																																						uc002omp.3																			1	Substitution - Missense(1)		upper_aerodigestive_tract(1)	ovary(4)|skin(4)|central_nervous_system(1)	9						c.(12991-12993)GCC>ACC		Fc fragment of IgG binding protein precursor		C	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	183.0	192.0	189.0		12991	3.0	0.8	19		189	1,8599	1.2+/-3.3	0,1,4299	no	missense	FCGBP	NM_003890.2	58	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	possibly-damaging	4331/5406	40368357	4,13002	2203	4300	6503	SO:0001583	missense	8857					extracellular region	protein binding	g.chr19:40368357C>T	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12991G>A	19.37:g.40368357C>T	ENSP00000221347:p.Ala4331Thr						p.A4331T	NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		28	12999	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		4331					O95784	Missense_Mutation	SNP	ENST00000221347.6	37	c.12991G>A	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	7.760	0.705270	0.15172	6.81E-4	1.16E-4	ENSG00000090920	ENST00000221347	T	0.78481	-1.18	4.08	3.0	0.34707	Uncharacterised domain, cysteine-rich (2);	0.495083	0.18716	U	0.133148	T	0.66237	0.2769	M	0.72624	2.21	0.20074	N	0.999938	P	0.39250	0.665	B	0.26864	0.074	T	0.59679	-0.7409	10	0.36615	T	0.2	.	4.2383	0.10637	0.0:0.6005:0.2058:0.1937	.	4331	Q9Y6R7	FCGBP_HUMAN	T	4331	ENSP00000221347:A4331T	ENSP00000221347:A4331T	A	-	1	0	FCGBP	45060197	0.000000	0.05858	0.755000	0.31263	0.082000	0.17680	-0.081000	0.11321	1.027000	0.39758	0.305000	0.20034	GCC		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
BCKDHA	593	broad.mit.edu	37	19	41932065	41932066	+	IGR	DEL	TG	TG	-			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:41932065_41932066delTG	ENST00000269980.2	+	0	2103				CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000601379.1_5'UTR|B3GNT8_ENST00000321702.2_Frame_Shift_Del_p.YS206fs	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						AGCAGGTCACTGTAGCGACGGC	0.653																																						uc002oqs.2																			0					0						c.(616-621)TACAGTfs		UDP-GlcNAc:betaGal																																				SO:0001628	intergenic_variant	374907				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity	g.chr19:41932065_41932066delTG	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932065_41932066delTG						CYP2F1_uc010xvw.1_Intron|B3GNT8_uc002oqt.1_Intron	p.Y206fs	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN			3	1072_1073	-			206_207			Lumenal (Potential).		B4DP47|E7EW46|Q16034|Q16472	Frame_Shift_Del	DEL	ENST00000269980.2	37	c.618_619delCA	CCDS12581.1																																																																																				0.653	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
GPR4	2828	broad.mit.edu	37	19	46094683	46094683	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:46094683C>T	ENST00000323040.4	-	2	1386	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	148					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		GCCGAGTTGGCGCCCAGCTCC	0.672																																					Esophageal Squamous(117;181 1612 1673 14956 42937)	uc002pcm.2																			0				ovary(2)	2						c.(442-444)GCC>ACC		G protein-coupled receptor 4							41.0	46.0	44.0					19																	46094683		2203	4299	6502	SO:0001583	missense	2828					integral to plasma membrane	G-protein coupled receptor activity	g.chr19:46094683C>T	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.442G>A	19.37:g.46094683C>T	ENSP00000319744:p.Ala148Thr					OPA3_uc010xxk.1_Intron	p.A148T	NM_005282	NP_005273	P46093	GPR4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)	2	1387	-			148			Helical; Name=4; (Potential).		A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000323040.4	37	c.442G>A	CCDS12669.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926490	0.34002	.	.	ENSG00000177464	ENST00000323040	T	0.72282	-0.64	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	T	0.61173	0.2326	L	0.37507	1.11	0.48762	D	0.999707	P	0.42123	0.771	B	0.38712	0.28	T	0.59490	-0.7445	10	0.21540	T	0.41	.	16.5114	0.84286	0.0:1.0:0.0:0.0	.	148	P46093	GPR4_HUMAN	T	148	ENSP00000319744:A148T	ENSP00000319744:A148T	A	-	1	0	GPR4	50786523	0.978000	0.34361	0.999000	0.59377	0.997000	0.91878	1.987000	0.40687	2.501000	0.84356	0.455000	0.32223	GCC		0.672	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
GPR4	2828	broad.mit.edu	37	19	46094825	46094825	+	Silent	SNP	A	A	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:46094825A>G	ENST00000323040.4	-	2	1244	c.300T>C	c.(298-300)aaT>aaC	p.N100N	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	100					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		TGATGTAGATATTGGTGTAGA	0.622																																					Esophageal Squamous(117;181 1612 1673 14956 42937)	uc002pcm.2																			0				ovary(2)	2						c.(298-300)AAT>AAC		G protein-coupled receptor 4							106.0	107.0	107.0					19																	46094825		2203	4300	6503	SO:0001819	synonymous_variant	2828					integral to plasma membrane	G-protein coupled receptor activity	g.chr19:46094825A>G	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.300T>C	19.37:g.46094825A>G						OPA3_uc010xxk.1_Intron	p.N100N	NM_005282	NP_005273	P46093	GPR4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)	2	1245	-			100			Helical; Name=3; (Potential).		A8K3T3|B0M0K1|Q6NWM4	Silent	SNP	ENST00000323040.4	37	c.300T>C	CCDS12669.1																																																																																				0.622	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
CCDC114	93233	broad.mit.edu	37	19	48807021	48807021	+	Missense_Mutation	SNP	C	C	T	rs571330368		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:48807021C>T	ENST00000315396.7	-	8	1445	c.763G>A	c.(763-765)Gtc>Atc	p.V255I		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	255					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		GTCTTCCAGACGCCCTCGGCC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.001					uc002pir.2																			0				ovary(1)	1						c.(763-765)GTC>ATC		coiled-coil domain containing 114 isoform 2																																				SO:0001583	missense	93233							g.chr19:48807021C>T	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.763G>A	19.37:g.48807021C>T	ENSP00000318429:p.Val255Ile					CCDC114_uc002piq.2_Missense_Mutation_p.V64I|CCDC114_uc002pio.2_Missense_Mutation_p.V292I|CCDC114_uc002pis.1_5'Flank|CCDC114_uc002pit.1_Missense_Mutation_p.V292I|CCDC114_uc002piu.1_Missense_Mutation_p.V292I	p.V255I	NM_144577	NP_653178	Q96M63	CC114_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)	8	1446	-		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)	255					Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	c.763G>A	CCDS12714.2	.	.	.	.	.	.	.	.	.	.	C	0.111	-1.138675	0.01742	.	.	ENSG00000105479	ENST00000315396	T	0.21734	1.99	3.02	0.682	0.17992	.	.	.	.	.	T	0.13713	0.0332	L	0.29908	0.895	0.19945	N	0.999942	B;B;B	0.26935	0.079;0.164;0.049	B;B;B	0.17098	0.016;0.017;0.011	T	0.22730	-1.0208	9	0.34782	T	0.22	-8.4759	9.0752	0.36517	0.0:0.4532:0.5468:0.0	.	48;255;255	Q96M63-4;Q96M63;Q96M63-5	.;CC114_HUMAN;.	I	255	ENSP00000318429:V255I	ENSP00000318429:V255I	V	-	1	0	CCDC114	53498833	0.744000	0.28250	0.968000	0.41197	0.274000	0.26718	0.784000	0.26816	0.134000	0.18681	-1.135000	0.01939	GTC		0.632	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
CD33	945	broad.mit.edu	37	19	51728525	51728525	+	Missense_Mutation	SNP	C	C	T	rs369307221		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:51728525C>T	ENST00000262262.4	+	2	110	c.89C>T	c.(88-90)aCg>aTg	p.T30M	CD33_ENST00000436584.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.T30M|CD33_ENST00000421133.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	30	Ig-like V-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	GAGTCAGTGACGGTACAGGAG	0.582																																						uc002pwa.2																			0					0						c.(88-90)ACG>ATG		CD33 antigen isoform 1 precursor	Gemtuzumab ozogamicin(DB00056)	C	,MET/THR,MET/THR	0,4406		0,0,2203	62.0	61.0	61.0		,89,89	1.3	0.1	19		61	3,8597		0,3,4297	no	intron,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	,81,81	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,probably-damaging,probably-damaging	,30/311,30/365	51728525	3,13003	2203	4300	6503	SO:0001583	missense	945				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	external side of plasma membrane|integral to plasma membrane	receptor activity|sugar binding	g.chr19:51728525C>T	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.89C>T	19.37:g.51728525C>T	ENSP00000262262:p.Thr30Met					CD33_uc010eos.1_Missense_Mutation_p.T30M|CD33_uc010eot.1_Intron|CD33_uc010eou.1_5'Flank	p.T30M	NM_001772	NP_001763	P20138	CD33_HUMAN		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	2	129	+		all_neural(266;0.0199)	30			Extracellular (Potential).|Ig-like V-type.		B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	c.89C>T	CCDS33084.1	.	.	.	.	.	.	.	.	.	.	.	9.534	1.111574	0.20714	0.0	3.49E-4	ENSG00000105383	ENST00000262262;ENST00000391796	T;T	0.51325	0.71;0.71	3.58	1.32	0.21799	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.685180	0.04251	U	0.338647	T	0.63546	0.2520	M	0.80746	2.51	0.21064	N	0.999793	D;D	0.59357	0.963;0.985	P;P	0.58172	0.555;0.834	T	0.33727	-0.9857	10	0.54805	T	0.06	.	4.2936	0.10890	0.2237:0.6525:0.0:0.1238	.	30;30	F8WAL2;P20138	.;CD33_HUMAN	M	30	ENSP00000262262:T30M;ENSP00000375673:T30M	ENSP00000262262:T30M	T	+	2	0	CD33	56420337	0.000000	0.05858	0.053000	0.19242	0.018000	0.09664	-1.484000	0.02316	0.299000	0.22661	-0.140000	0.14226	ACG		0.582	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
CD33	945	broad.mit.edu	37	19	51729331	51729331	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr19:51729331G>A	ENST00000262262.4	+	3	712	c.691G>A	c.(691-693)Gtc>Atc	p.V231I	CD33_ENST00000436584.2_Missense_Mutation_p.V104I|CD33_ENST00000391796.3_Missense_Mutation_p.V231I|CD33_ENST00000421133.2_Missense_Mutation_p.V104I	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	231					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CCAGCTCAACGTCACCTGTAA	0.607																																						uc002pwa.2																			0					0						c.(691-693)GTC>ATC		CD33 antigen isoform 1 precursor	Gemtuzumab ozogamicin(DB00056)						38.0	36.0	37.0					19																	51729331		2203	4300	6503	SO:0001583	missense	945				cell adhesion|cell-cell signaling|negative regulation of cell proliferation	external side of plasma membrane|integral to plasma membrane	receptor activity|sugar binding	g.chr19:51729331G>A	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.691G>A	19.37:g.51729331G>A	ENSP00000262262:p.Val231Ile					CD33_uc010eos.1_Missense_Mutation_p.V231I|CD33_uc010eot.1_Missense_Mutation_p.V104I|CD33_uc010eou.1_RNA	p.V231I	NM_001772	NP_001763	P20138	CD33_HUMAN		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	3	731	+		all_neural(266;0.0199)	231			Extracellular (Potential).		B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	c.691G>A	CCDS33084.1	.	.	.	.	.	.	.	.	.	.	.	12.93	2.085191	0.36758	.	.	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.64803	-0.12;1.16;0.18;0.82	3.08	0.909	0.19332	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.30791	U	0.008875	T	0.62962	0.2471	M	0.69463	2.115	0.09310	N	1	P;D;P	0.54397	0.884;0.966;0.778	P;P;B	0.52881	0.699;0.712;0.222	T	0.54316	-0.8312	10	0.59425	D	0.04	.	4.6962	0.12804	0.306:0.0:0.694:0.0	.	104;231;231	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	I	104;231;104;231	ENSP00000403331:V104I;ENSP00000262262:V231I;ENSP00000410126:V104I;ENSP00000375673:V231I	ENSP00000262262:V231I	V	+	1	0	CD33	56421143	0.286000	0.24305	0.010000	0.14722	0.003000	0.03518	2.516000	0.45520	0.629000	0.30376	0.462000	0.41574	GTC		0.607	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
LINC01317	104355287	broad.mit.edu	37	2	33952147	33952147	+	lincRNA	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr2:33952147G>A	ENST00000366209.2	+	0	68				MYADML_ENST00000474610.1_RNA																							ACACCAGGTCGCCCACATAGG	0.577																																						uc002rpb.2																			0					0						c.(694-696)GGC>GGT		RecName: Full=Myeloid-associated differentiation marker-like protein.;																																						151325							g.chr2:33952147G>A																													2.37:g.33952147G>A							p.G232G	NR_003143						1	1138	-									Silent	SNP	ENST00000366209.2	37	c.696C>T																																																																																					0.577	AC009499.1-002	KNOWN	non_canonical_polymorphism|basic	lincRNA	lincRNA	OTTHUMT00000325406.1		
CPS1	1373	broad.mit.edu	37	2	211481222	211481222	+	Missense_Mutation	SNP	C	C	T	rs148519116		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr2:211481222C>T	ENST00000233072.5	+	21	2840	c.2644C>T	c.(2644-2646)Cgt>Tgt	p.R882C	CPS1_ENST00000451903.2_Missense_Mutation_p.R431C|CPS1_ENST00000430249.2_Missense_Mutation_p.R888C	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	882					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GTATAAGATGCGTGATATTTT	0.408																																						uc002vee.3																			0				ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13						c.(2644-2646)CGT>TGT		carbamoyl-phosphate synthetase 1 isoform b		C	CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	159.0	159.0	159.0		2662,1291,2644	4.6	1.0	2	dbSNP_134	159	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	888/1507,431/1050,882/1501	211481222	1,13005	2203	4300	6503	SO:0001583	missense	1373				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity	g.chr2:211481222C>T	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2644C>T	2.37:g.211481222C>T	ENSP00000233072:p.Arg882Cys					CPS1_uc010fur.2_Missense_Mutation_p.R888C|CPS1_uc010fus.2_Missense_Mutation_p.R431C|LOC29034_uc002vef.2_5'Flank	p.R882C	NM_001875	NP_001866	P31327	CPSM_HUMAN		Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	21	2776	+			882					B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	c.2644C>T	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.945930	0.73672	0.0	1.16E-4	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.96802	-4.13;-4.13;-4.13	5.52	4.63	0.57726	Carbamoyl-phosphate synthetase, large subunit, oligomerisation (3);	0.232221	0.45867	D	0.000326	D	0.97374	0.9141	M	0.77712	2.385	0.48135	D	0.999598	D;D	0.76494	0.999;0.999	P;P	0.56916	0.809;0.809	D	0.97812	1.0251	10	0.87932	D	0	-17.2182	15.883	0.79216	0.1366:0.8634:0.0:0.0	.	892;882	Q59HF8;P31327	.;CPSM_HUMAN	C	888;890;882;431	ENSP00000402608:R888C;ENSP00000233072:R882C;ENSP00000406136:R431C	ENSP00000233072:R882C	R	+	1	0	CPS1	211189467	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.783000	0.47766	1.426000	0.47256	0.655000	0.94253	CGT		0.408	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
NCL	4691	broad.mit.edu	37	2	232326477	232326477	+	Silent	SNP	G	G	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr2:232326477G>T	ENST00000322723.4	-	3	627	c.387C>A	c.(385-387)atC>atA	p.I129I	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	129	8 X 8 AA tandem repeats of X-T-P-X-K-K-X- X.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CCTTGGCTGGGATGGCAGCAC	0.532																																						uc002vru.2																			0				ovary(2)|pancreas(1)	3						c.(385-387)ATC>ATA		nucleolin							341.0	241.0	275.0					2																	232326477		2203	4300	6503	SO:0001819	synonymous_variant	4691				angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding	g.chr2:232326477G>T		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.387C>A	2.37:g.232326477G>T						SNORD82_uc010fxw.1_5'Flank	p.I129I	NM_005381	NP_005372	P19338	NUCL_HUMAN		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)	3	528	-		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)	129			8.|8 X 8 AA tandem repeats of X-T-P-X-K-K-X- X.		Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	c.387C>A	CCDS33397.1																																																																																				0.532	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
SH3BP4	23677	broad.mit.edu	37	2	235950763	235950763	+	Silent	SNP	C	C	T	rs201095699		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr2:235950763C>T	ENST00000409212.1	+	4	1857	c.1350C>T	c.(1348-1350)taC>taT	p.Y450Y	SH3BP4_ENST00000392011.2_Silent_p.Y450Y|SH3BP4_ENST00000344528.4_Silent_p.Y450Y			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	450					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCTGTATGTACGTGGCTGTCG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		18541	0.001		0.0	False		,,,				2504	0.0					uc002vvp.2																			0				skin(3)|ovary(1)	4						c.(1348-1350)TAC>TAT		SH3-domain binding protein 4		C		0,4406		0,0,2203	53.0	49.0	50.0		1350	4.7	1.0	2		50	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	SH3BP4	NM_014521.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		450/964	235950763	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23677				endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding	g.chr2:235950763C>T	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1350C>T	2.37:g.235950763C>T						SH3BP4_uc010fym.2_Silent_p.Y450Y|SH3BP4_uc002vvq.2_Silent_p.Y450Y	p.Y450Y	NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)	4	1743	+		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)	450					O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	c.1350C>T	CCDS2513.1																																																																																				0.577	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
D2HGDH	728294	broad.mit.edu	37	2	242683167	242683167	+	Silent	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr2:242683167C>T	ENST00000321264.4	+	5	830	c.621C>T	c.(619-621)aaC>aaT	p.N207N	D2HGDH_ENST00000537090.1_Silent_p.N207N|D2HGDH_ENST00000342518.6_Silent_p.N207N|D2HGDH_ENST00000403782.1_Silent_p.N73N	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	207	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TGGCAACCAACGCTGGAGGCC	0.617																																						uc002wce.1																			0					0						c.(619-621)AAC>AAT		D-2-hydroxyglutarate dehydrogenase precursor							55.0	49.0	51.0					2																	242683167		2203	4296	6499	SO:0001819	synonymous_variant	728294				2-oxoglutarate metabolic process|cellular protein metabolic process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding	g.chr2:242683167C>T	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.621C>T	2.37:g.242683167C>T						D2HGDH_uc010zpc.1_RNA|D2HGDH_uc010fzq.1_Silent_p.N73N|D2HGDH_uc002wcg.1_RNA	p.N207N	NM_152783	NP_689996	Q8N465	D2HDH_HUMAN		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)	5	794	+		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)	207			FAD-binding PCMH-type.		B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Silent	SNP	ENST00000321264.4	37	c.621C>T	CCDS33426.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102153	0.37048	.	.	ENSG00000180902	ENST00000417686	.	.	.	5.15	-9.44	0.00603	.	.	.	.	.	T	0.64843	0.2635	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73579	-0.3938	4	.	.	.	.	18.7541	0.91826	0.0:0.2568:0.0:0.7432	.	.	.	.	C	49	.	.	R	+	1	0	D2HGDH	242331840	0.000000	0.05858	0.060000	0.19600	0.607000	0.37147	-2.323000	0.01117	-1.917000	0.01074	0.462000	0.41574	CGC		0.617	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
SEMG2	6407	broad.mit.edu	37	20	43851621	43851621	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr20:43851621G>A	ENST00000372769.3	+	2	1438	c.1348G>A	c.(1348-1350)Gta>Ata	p.V450I		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	450	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				TCAAAACCAGGTAACAATTCC	0.383																																						uc010ggz.2																			0				skin(1)	1						c.(1348-1350)GTA>ATA		semenogelin II precursor							79.0	77.0	78.0					20																	43851621		2203	4300	6503	SO:0001583	missense	6407				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity	g.chr20:43851621G>A		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1348G>A	20.37:g.43851621G>A	ENSP00000361855:p.Val450Ile					SEMG2_uc002xnk.2_Missense_Mutation_p.V450I|SEMG2_uc002xnl.2_Intron	p.V450I	NM_003008	NP_002999	Q02383	SEMG2_HUMAN			2	1405	+		Myeloproliferative disorder(115;0.0122)	450			Repeat-rich region.|4 X 60 AA tandem repeats, type I.		Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	c.1348G>A	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	G	1.528	-0.545186	0.04024	.	.	ENSG00000124157	ENST00000372769	T	0.06768	3.26	1.25	0.0886	0.14455	.	.	.	.	.	T	0.02848	0.0085	N	0.03608	-0.345	0.09310	N	1	B;B	0.16802	0.001;0.019	B;B	0.23419	0.013;0.046	T	0.48007	-0.9072	9	0.10902	T	0.67	.	2.9627	0.05897	0.6654:0.0:0.3346:0.0	.	450;450	A8K6Z6;Q02383	.;SEMG2_HUMAN	I	450	ENSP00000361855:V450I	ENSP00000361855:V450I	V	+	1	0	SEMG2	43285035	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.489000	0.06490	-0.008000	0.14320	-0.471000	0.05019	GTA		0.383	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
SULF2	55959	broad.mit.edu	37	20	46292214	46292214	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr20:46292214G>A	ENST00000359930.4	-	16	3061	c.2210C>T	c.(2209-2211)aCg>aTg	p.T737M	SULF2_ENST00000361612.4_Missense_Mutation_p.T737M|SULF2_ENST00000484875.1_Missense_Mutation_p.T737M|SULF2_ENST00000467815.1_Missense_Mutation_p.T737M	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	737					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GAAAGGCGCCGTCTGCCAGTG	0.597											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002xto.2																			0				ovary(2)|breast(2)|pancreas(1)|skin(1)	6						c.(2209-2211)ACG>ATG		sulfatase 2 isoform a precursor							99.0	90.0	93.0					20																	46292214		2203	4300	6503	SO:0001583	missense	55959				bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding	g.chr20:46292214G>A	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2210C>T	20.37:g.46292214G>A	ENSP00000353007:p.Thr737Met		OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	938	SULF2_uc002xtr.2_Missense_Mutation_p.T737M|SULF2_uc002xtq.2_Missense_Mutation_p.T737M|SULF2_uc010zyd.1_Missense_Mutation_p.T16M	p.T737M	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN			16	2540	-			737					E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	c.2210C>T	CCDS13408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.623960|4.623960	0.87560|0.87560	.|.	.|.	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.25749	.|1.78;1.78;1.78;1.78	5.94|5.94	5.94|5.94	0.96194|0.96194	.|Alkaline-phosphatase-like, core domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60418|0.60418	0.2267|0.2267	M|M	0.87971|0.87971	2.92|2.92	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.998	T|T	0.64647|0.64647	-0.6358|-0.6358	5|10	.|0.87932	.|D	.|0	-18.5879|-18.5879	20.3632|20.3632	0.98871|0.98871	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|737;737	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	W|M	92|737;737;737;156;737	.|ENSP00000353007:T737M;ENSP00000418290:T737M;ENSP00000354662:T737M;ENSP00000418442:T737M	.|ENSP00000353007:T737M	R|T	-|-	1|2	2|0	SULF2|SULF2	45725621|45725621	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.576000|0.576000	0.36127|0.36127	9.869000|9.869000	0.99810|0.99810	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	CGG|ACG		0.597	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
ZFP64	55734	broad.mit.edu	37	20	50803594	50803594	+	Silent	SNP	C	C	T	rs529661940		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr20:50803594C>T	ENST00000216923.4	-	2	412	c.63G>A	c.(61-63)acG>acA	p.T21T	ZFP64_ENST00000371518.2_Silent_p.T21T|ZFP64_ENST00000361387.2_Silent_p.T21T|ZFP64_ENST00000371515.4_Silent_p.T19T|ZFP64_ENST00000346617.4_Silent_p.T21T	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	21					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CCACCAGCACCGTTGTGCCAC	0.483													C|||	1	0.000199681	0.0	0.0	5008	,	,		19795	0.001		0.0	False		,,,				2504	0.0					uc002xwl.2																			0				upper_aerodigestive_tract(1)|ovary(1)	2						c.(61-63)ACG>ACA		zinc finger protein 64 isoform a							59.0	53.0	55.0					20																	50803594		2203	4300	6503	SO:0001819	synonymous_variant	55734				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr20:50803594C>T	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.63G>A	20.37:g.50803594C>T						ZFP64_uc002xwk.2_Silent_p.T21T|ZFP64_uc002xwm.2_Silent_p.T19T|ZFP64_uc002xwn.2_Silent_p.T21T	p.T21T	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN			2	412	-			21					Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	c.63G>A	CCDS13440.1																																																																																				0.483	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
LAMA5	3911	broad.mit.edu	37	20	60921843	60921843	+	Silent	SNP	G	G	A	rs373700695		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr20:60921843G>A	ENST00000252999.3	-	8	1152	c.1086C>T	c.(1084-1086)taC>taT	p.Y362Y	LAMA5_ENST00000370677.3_Silent_p.Y362Y|LAMA5_ENST00000370692.3_Silent_p.Y362Y	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	362	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGGCATGGCCGTAGCAGTTAC	0.667																																						uc002ycq.2																			0				ovary(1)|pancreas(1)|skin(1)	3						c.(1084-1086)TAC>TAT		laminin alpha 5 precursor	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	A		1,4397	2.1+/-5.4	0,1,2198	29.0	32.0	31.0		1086	-9.7	0.3	20		31	0,8590		0,0,4295	no	coding-synonymous	LAMA5	NM_005560.3		0,1,6493	AA,AG,GG		0.0,0.0227,0.0077		362/3696	60921843	1,12987	2199	4295	6494	SO:0001819	synonymous_variant	3911				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding	g.chr20:60921843G>A	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.1086C>T	20.37:g.60921843G>A							p.Y362Y	NM_005560	NP_005551	O15230	LAMA5_HUMAN	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		8	1153	-	Breast(26;1.57e-08)		362			Laminin EGF-like 2.		Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	c.1086C>T	CCDS33502.1																																																																																				0.667	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
TMPRSS15	5651	broad.mit.edu	37	21	19770222	19770222	+	Silent	SNP	A	A	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr21:19770222A>G	ENST00000284885.3	-	3	351	c.318T>C	c.(316-318)taT>taC	p.Y106Y		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	106	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TTGAGTTCTTATATTCATTCT	0.249																																						uc002ykw.2																			0				ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						c.(316-318)TAT>TAC		enterokinase precursor							16.0	17.0	17.0					21																	19770222		2132	4212	6344	SO:0001819	synonymous_variant	5651				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity	g.chr21:19770222A>G		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.318T>C	21.37:g.19770222A>G							p.Y106Y	NM_002772	NP_002763	P98073	ENTK_HUMAN			3	349	-			106			Extracellular (Potential).|SEA.		Q2NKL7	Silent	SNP	ENST00000284885.3	37	c.318T>C	CCDS13571.1																																																																																				0.249	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
RIPK4	54101	broad.mit.edu	37	21	43161519	43161519	+	Missense_Mutation	SNP	C	C	T	rs371705604		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr21:43161519C>T	ENST00000352483.2	-	9	2042	c.1978G>A	c.(1978-1980)Gca>Aca	p.A660T	AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Missense_Mutation_p.A612T|RIPK4_ENST00000542057.1_Missense_Mutation_p.A549T|RIPK4_ENST00000544709.1_Missense_Mutation_p.A549T			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	660					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CCGCGCTGTGCGGCCAGGTGC	0.687																																						uc002yzn.1																			0				ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7						c.(1834-1836)GCA>ACA		ankyrin repeat domain 3							59.0	60.0	60.0					21																	43161519		2203	4298	6501	SO:0001583	missense	54101					cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity	g.chr21:43161519C>T	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1978G>A	21.37:g.43161519C>T	ENSP00000330161:p.Ala660Thr						p.A612T	NM_020639	NP_065690	P57078	RIPK4_HUMAN			8	1882	-			612					Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37	c.1834G>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.24|15.24	2.775232|2.775232	0.49786|0.49786	.|.	.|.	ENSG00000183421|ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057|ENST00000330470	T;T;T;T|.	0.69040|.	-0.37;-0.33;1.89;1.89|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.000000|.	0.64402|.	D|.	0.000009|.	T|T	0.66187|0.66187	0.2764|0.2764	M|M	0.66439|0.66439	2.03|2.03	0.42100|0.42100	D|D	0.991336|0.991336	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.63157|0.63157	-0.6700|-0.6700	10|6	0.49607|0.02654	T|T	0.09|1	-31.9783|-31.9783	17.2557|17.2557	0.87056|0.87056	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	612|.	P57078-2|.	.|.	T|H	612;660;549;549|348	ENSP00000332454:A612T;ENSP00000330161:A660T;ENSP00000441754:A549T;ENSP00000442901:A549T|.	ENSP00000332454:A612T|ENSP00000330975:R348H	A|R	-|-	1|2	0|0	RIPK4|RIPK4	42034588|42034588	0.997000|0.997000	0.39634|0.39634	0.880000|0.880000	0.34516|0.34516	0.173000|0.173000	0.22820|0.22820	3.632000|3.632000	0.54287|0.54287	2.298000|2.298000	0.77334|0.77334	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.687	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
A4GALT	53947	broad.mit.edu	37	22	43089430	43089430	+	Silent	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr22:43089430G>A	ENST00000401850.1	-	2	1017	c.528C>T	c.(526-528)gaC>gaT	p.D176D	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000381278.3_Silent_p.D176D|A4GALT_ENST00000249005.2_Silent_p.D176D			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	176					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						TCCTGGAGGCGTCGGAGAGCA	0.652																																						uc003bdb.2																			0				central_nervous_system(2)	2						c.(526-528)GAC>GAT		alpha 1,4-galactosyltransferase							55.0	52.0	53.0					22																	43089430		2203	4300	6503	SO:0001819	synonymous_variant	53947				glycosphingolipid biosynthetic process|plasma membrane organization	Golgi stack|integral to Golgi membrane|membrane fraction	lactosylceramide 4-alpha-galactosyltransferase activity	g.chr22:43089430G>A		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.528C>T	22.37:g.43089430G>A						A4GALT_uc010gzd.2_Silent_p.D176D	p.D176D	NM_017436	NP_059132	Q9NPC4	A4GAT_HUMAN			3	789	-			176			Lumenal (Potential).		B2R7C4|Q9P1X5	Silent	SNP	ENST00000401850.1	37	c.528C>T	CCDS14041.1																																																																																				0.652	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
SHANK3	85358	broad.mit.edu	37	22	51159629	51159629	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr22:51159629C>T	ENST00000414786.2	+	21	3553	c.3326C>T	c.(3325-3327)gCg>gTg	p.A1109V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A1139V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A1125V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1123					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GCCTCCCAGGCGCCCTCCCGG	0.711																																						uc003bne.1																			0				central_nervous_system(1)	1						c.(3415-3417)GCG>GTG		SH3 and multiple ankyrin repeat domains 3							9.0	11.0	10.0					22																	51159629		1945	4098	6043	SO:0001583	missense	85358							g.chr22:51159629C>T	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3326C>T	22.37:g.51159629C>T	ENSP00000464552:p.Ala1109Val					SHANK3_uc003bnf.1_Missense_Mutation_p.A586V|SHANK3_uc010hbg.1_Missense_Mutation_p.A321V	p.A1139V	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN		BRCA - Breast invasive adenocarcinoma(115;0.22)	22	3416	+		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)	1139					D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37	c.3416C>T		.	.	.	.	.	.	.	.	.	.	C	8.902	0.956689	0.18507	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.22539	1.95;1.95	4.3	1.72	0.24424	.	0.449310	0.24559	N	0.037481	T	0.09024	0.0223	N	0.04880	-0.145	0.09310	N	0.99999	B;B;B	0.15473	0.0;0.013;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.30592	-0.9973	10	0.28530	T	0.3	.	9.1874	0.37178	0.0:0.7827:0.0:0.2173	.	1123;1124;1139	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1139;1125	ENSP00000442518:A1139V;ENSP00000446078:A1125V	ENSP00000442518:A1139V	A	+	2	0	SHANK3	49506495	0.178000	0.23122	0.853000	0.33588	0.852000	0.48524	0.424000	0.21330	0.802000	0.34089	0.462000	0.41574	GCG		0.711	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
CNTN6	27255	broad.mit.edu	37	3	1418745	1418745	+	Missense_Mutation	SNP	G	G	A	rs140014929		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr3:1418745G>A	ENST00000446702.2	+	17	2779	c.2152G>A	c.(2152-2154)Gtc>Atc	p.V718I	CNTN6_ENST00000350110.2_Missense_Mutation_p.V718I|CNTN6_ENST00000539053.1_Missense_Mutation_p.V646I			Q9UQ52	CNTN6_HUMAN	contactin 6	718	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.V718I(2)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GTCTGAACTCGTCATTACGTG	0.373																																						uc003boz.2																			2	Substitution - Missense(2)	p.V718I(1)	large_intestine(1)|pancreas(1)	skin(3)|lung(2)|breast(2)|pancreas(1)	8						c.(2152-2154)GTC>ATC		contactin 6 precursor		G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	188.0	178.0	182.0		2152	-0.1	1.0	3	dbSNP_134	182	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTN6	NM_014461.2	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	718/1029	1418745	2,13004	2203	4300	6503	SO:0001583	missense	27255				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane		g.chr3:1418745G>A	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2152G>A	3.37:g.1418745G>A	ENSP00000407822:p.Val718Ile					CNTN6_uc011asj.1_Missense_Mutation_p.V646I|CNTN6_uc003bpa.2_Missense_Mutation_p.V718I	p.V718I	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)	17	2419	+		all_cancers(2;0.000164)|all_epithelial(2;0.107)	718			Fibronectin type-III 2.		Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	c.2152G>A	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392335	0.42410	2.27E-4	1.16E-4	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.53857	0.6;0.6;0.6	5.76	-0.13	0.13498	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.235772	0.29684	N	0.011465	T	0.40372	0.1114	L	0.43152	1.355	0.44395	D	0.997306	B	0.15930	0.015	B	0.10450	0.005	T	0.20405	-1.0276	10	0.32370	T	0.25	.	11.0846	0.48080	0.3437:0.0:0.6563:0.0	.	718	Q9UQ52	CNTN6_HUMAN	I	718;646;718	ENSP00000407822:V718I;ENSP00000442791:V646I;ENSP00000341882:V718I	ENSP00000341882:V718I	V	+	1	0	CNTN6	1393745	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	3.636000	0.54317	0.098000	0.17522	0.655000	0.94253	GTC		0.373	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
RARB	5915	broad.mit.edu	37	3	25215958	25215958	+	Missense_Mutation	SNP	C	C	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr3:25215958C>A	ENST00000404969.1	+	1	70	c.70C>A	c.(70-72)Ccc>Acc	p.P24T	AC133680.1_ENST00000455576.1_lincRNA			P10826	RARB_HUMAN	retinoic acid receptor, beta	24	Modulating.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TCCAGCCACACCCTACCCGTT	0.592																																						uc011awl.1																			0				ovary(1)|large_intestine(1)|pancreas(1)	3						c.(70-72)CCC>ACC		retinoic acid receptor, beta isoform 2	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)						188.0	163.0	171.0					3																	25215958		876	1991	2867	SO:0001583	missense	5915				embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	g.chr3:25215958C>A	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.70C>A	3.37:g.25215958C>A	ENSP00000385865:p.Pro24Thr						p.P24T	NM_016152	NP_057236	P10826	RARB_HUMAN			1	136	+			24			Modulating.		P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37	c.70C>A		.	.	.	.	.	.	.	.	.	.	C	15.65	2.896759	0.52121	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226	D;D	0.92299	-2.8;-3.01	5.88	5.88	0.94601	.	.	.	.	.	D	0.90335	0.6976	.	.	.	0.38203	D	0.940252	B	0.22604	0.072	B	0.17722	0.019	D	0.86986	0.2107	8	0.56958	D	0.05	.	20.2187	0.98312	0.0:1.0:0.0:0.0	.	24	P10826	RARB_HUMAN	T	24	ENSP00000373282:P24T;ENSP00000385865:P24T	ENSP00000373282:P24T	P	+	1	0	RARB	25190962	0.999000	0.42202	0.968000	0.41197	0.830000	0.47004	5.359000	0.66074	2.780000	0.95670	0.655000	0.94253	CCC		0.592	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152	
CYP8B1	1582	broad.mit.edu	37	3	42916827	42916827	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr3:42916827G>A	ENST00000316161.4	-	1	806	c.482C>T	c.(481-483)gCc>gTc	p.A161V	RP11-141M3.5_ENST00000471537.1_RNA|KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.A161V	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	161					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CCAGCAACTGGCATCCAGACT	0.522																																						uc003cmh.2																			0				ovary(2)	2						c.(481-483)GCC>GTC		cytochrome P450, family 8, subfamily B,							84.0	77.0	79.0					3																	42916827		2203	4300	6503	SO:0001583	missense	1582				bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity	g.chr3:42916827G>A	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.482C>T	3.37:g.42916827G>A	ENSP00000318867:p.Ala161Val					CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Missense_Mutation_p.A161V	p.A161V	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)	1	807	-			161					B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	c.482C>T	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.704017	0.30232	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.66815	-0.23;-0.23	5.03	3.06	0.35304	.	0.731043	0.13175	N	0.407974	T	0.65709	0.2717	L	0.58101	1.795	0.09310	N	1	P;B	0.41188	0.741;0.436	B;B	0.43018	0.405;0.315	T	0.53351	-0.8451	10	0.36615	T	0.2	-10.2214	12.3238	0.54999	0.0:0.0:0.3467:0.6533	.	161;161	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	V	161	ENSP00000404499:A161V;ENSP00000318867:A161V	ENSP00000318867:A161V	A	-	2	0	CYP8B1	42891831	0.563000	0.26594	0.001000	0.08648	0.333000	0.28666	2.269000	0.43346	0.542000	0.28846	0.555000	0.69702	GCC		0.522	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
WHSC1	7468	broad.mit.edu	37	4	1955109	1955109	+	Silent	SNP	A	A	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr4:1955109A>G	ENST00000382895.3	+	14	2627	c.2196A>G	c.(2194-2196)gtA>gtG	p.V732V	WHSC1_ENST00000508803.1_Silent_p.V732V|WHSC1_ENST00000382892.2_Silent_p.V732V|WHSC1_ENST00000382891.5_Silent_p.V732V|WHSC1_ENST00000382888.3_Silent_p.V80V|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	732					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GCTGTGTGGTAACTCAGTGTG	0.458			T	IGH@	MM																																	uc003gdz.3				Dom	yes		4	4p16.3	7468	T	Wolf-Hirschhorn syndrome candidate 1(MMSET)			L	IGH@		MM		0				ovary(3)|lung(3)|skin(2)|pancreas(1)	9						c.(2194-2196)GTA>GTG		Wolf-Hirschhorn syndrome candidate 1 protein							148.0	153.0	151.0					4																	1955109		2203	4300	6503	SO:0001819	synonymous_variant	7468				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding	g.chr4:1955109A>G	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2196A>G	4.37:g.1955109A>G						WHSC1_uc003geb.3_Silent_p.V732V|WHSC1_uc003gec.3_Silent_p.V732V|WHSC1_uc003ged.3_Silent_p.V732V|WHSC1_uc003gee.3_RNA|WHSC1_uc003gef.3_RNA|WHSC1_uc003gei.3_5'UTR|WHSC1_uc011bvh.1_5'UTR|WHSC1_uc010icf.2_Silent_p.V80V	p.V732V	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)	12	2372	+		all_epithelial(65;1.34e-05)	732			PHD-type 2.		A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Silent	SNP	ENST00000382895.3	37	c.2196A>G	CCDS33940.1																																																																																				0.458	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
PAM	5066	broad.mit.edu	37	5	102360910	102360911	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr5:102360910_102360911delAG	ENST00000438793.3	+	23	3031_3032	c.2561_2562delAG	c.(2560-2562)cagfs	p.Q854fs	PAM_ENST00000346918.2_Intron|PAM_ENST00000455264.2_Intron|PAM_ENST00000379787.4_Frame_Shift_Del_p.Q234fs|PAM_ENST00000304400.7_Frame_Shift_Del_p.Q854fs|PAM_ENST00000348126.2_Frame_Shift_Del_p.Q747fs|PAM_ENST00000274392.9_Frame_Shift_Del_p.Q756fs	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	854					central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CAAGAGAAACAGAAACTGATCA	0.46																																						uc003knw.2																			0					0						c.(2560-2562)CAGfs		peptidylglycine alpha-amidating monooxygenase	Vitamin C(DB00126)																																			SO:0001589	frameshift_variant	5066				peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding	g.chr5:102360910_102360911delAG	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"""peptidyl-alpha-hydroxyglycine alpha-amidating lyase"", ""peptidylglycine alpha-hydroxylating monooxygenase"""	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.2561_2562delAG	5.37:g.102360910_102360911delAG	ENSP00000396493:p.Gln854fs					PAM_uc003kns.2_Frame_Shift_Del_p.Q747fs|PAM_uc003knt.2_Frame_Shift_Del_p.Q854fs|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Frame_Shift_Del_p.Q756fs|PAM_uc003knz.2_Frame_Shift_Del_p.Q94fs	p.Q854fs	NM_000919	NP_000910	P19021	AMD_HUMAN		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	23	2934_2935	+		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)	854			Intragranular (Potential).		A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Frame_Shift_Del	DEL	ENST00000438793.3	37	c.2561_2562delAG	CCDS54885.1																																																																																				0.460	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	
PKHD1	5314	broad.mit.edu	37	6	51523917	51523917	+	Silent	SNP	C	C	T	rs142855690		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr6:51523917C>T	ENST00000371117.3	-	61	11282	c.11007G>A	c.(11005-11007)tcG>tcA	p.S3669S		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3669					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TTACTGTTGGCGAATCACCAA	0.423													c|||	1	0.000199681	0.0	0.0	5008	,	,		20393	0.0		0.001	False		,,,				2504	0.0					uc003pah.1																			0				lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44						c.(11005-11007)TCG>TCA		fibrocystin isoform 1		G		0,4406		0,0,2203	173.0	159.0	164.0		11007	-3.1	0.0	6	dbSNP_134	164	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PKHD1	NM_138694.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		3669/4075	51523917	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5314				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	g.chr6:51523917C>T	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11007G>A	6.37:g.51523917C>T							p.S3669S	NM_138694	NP_619639	P08F94	PKHD1_HUMAN			61	11283	-	Lung NSC(77;0.0605)		3669			Extracellular (Potential).		Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	c.11007G>A	CCDS4935.1																																																																																				0.423	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
TRAF3IP2	10758	broad.mit.edu	37	6	111912560	111912560	+	Missense_Mutation	SNP	A	A	G			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr6:111912560A>G	ENST00000340026.6	-	3	1351	c.757T>C	c.(757-759)Tat>Cat	p.Y253H	TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.Y244H|TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.Y244H			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	253	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		CATGCTGGATACCTCTGAGGT	0.572																																						uc011ebc.1																			0				ovary(2)|central_nervous_system(1)	3						c.(730-732)TAT>CAT		TRAF3 interacting protein 2 isoform 2							91.0	87.0	88.0					6																	111912560		2203	4300	6503	SO:0001583	missense	10758				intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular		g.chr6:111912560A>G	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"""chromosome 6 open reading frame 5"", ""chromosome 6 open reading frame 2"""	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.757T>C	6.37:g.111912560A>G	ENSP00000345984:p.Tyr253His					TRAF3IP2_uc003pvg.2_Missense_Mutation_p.Y244H|TRAF3IP2_uc003pvf.2_Missense_Mutation_p.Y244H|TRAF3IP2_uc010kdw.2_Missense_Mutation_p.Y244H|TRAF3IP2_uc010kdx.2_Missense_Mutation_p.Y244H	p.Y244H	NM_147686	NP_679211	O43734	CIKS_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)	3	1345	-		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)	253					B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37	c.730T>C		.	.	.	.	.	.	.	.	.	.	A	8.004	0.755960	0.15846	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.35236	1.33;1.33;1.32	5.84	3.44	0.39384	.	0.251301	0.35235	N	0.003345	T	0.11922	0.0290	L	0.46157	1.445	0.26981	N	0.96536	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.09377	0.002;0.004;0.002	T	0.21143	-1.0254	10	0.20046	T	0.44	23.2443	9.2203	0.37373	0.7933:0.0:0.2067:0.0	.	253;244;244	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	H	253;244;253;244	ENSP00000357750:Y244H;ENSP00000345984:Y253H;ENSP00000352889:Y244H	ENSP00000345984:Y253H	Y	-	1	0	TRAF3IP2	112019253	0.640000	0.27243	0.321000	0.25320	0.734000	0.41952	2.032000	0.41127	1.041000	0.40125	0.454000	0.30748	TAT		0.572	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2		
DPY19L2P1	554236	broad.mit.edu	37	7	35130052	35130052	+	RNA	SNP	C	C	T	rs555354370		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:35130052C>T	ENST00000436258.1	-	0	3317							Q6NXN4	D19P1_HUMAN	DPY19L2 pseudogene 1							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										TATTTTTGTCCGAGCCCTTTA	0.264																																						uc003teq.1																			0					0						c.(1132-1134)CGG>CAG		RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;																																						554236							g.chr7:35130052C>T	BC066987		7p14.2	2014-03-18	2013-09-12		ENSG00000189212	ENSG00000189212			22305	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 1 (C. elegans)"""				Standard	NR_002833		Approved		uc031swy.1	Q6NXN4	OTTHUMG00000155026		7.37:g.35130052C>T						DPY19L2P1_uc003tep.1_RNA|DPY19L2P1_uc010kwz.1_RNA	p.R378Q							21	2240	-								B4E2E3	Missense_Mutation	SNP	ENST00000436258.1	37	c.1133G>A																																																																																					0.264	DPY19L2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000338113.1		
PON1	5444	broad.mit.edu	37	7	94953757	94953757	+	Missense_Mutation	SNP	C	C	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:94953757C>A	ENST00000222381.3	-	1	262	c.31G>T	c.(31-33)Ggg>Tgg	p.G11W	PON1_ENST00000542556.1_Intron	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	11					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	AGTCCCATCCCCAAGAGGGTG	0.607																																					GBM(119;715 1622 17358 22490 33240)	uc003uns.2																			0				pancreas(1)	1						c.(31-33)GGG>TGG		paraoxonase 1 precursor	Atorvastatin(DB01076)|Cefazolin(DB01327)						138.0	100.0	113.0					7																	94953757		2203	4300	6503	SO:0001583	missense	5444				aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity	g.chr7:94953757C>A	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.31G>T	7.37:g.94953757C>A	ENSP00000222381:p.Gly11Trp					PON1_uc011kih.1_Intron	p.G11W	NM_000446	NP_000437	P27169	PON1_HUMAN	STAD - Stomach adenocarcinoma(171;0.0031)		1	128	-	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		11					B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	c.31G>T	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485207	0.26598	.	.	ENSG00000005421	ENST00000222381	T	0.56275	0.47	4.31	3.43	0.39272	Six-bladed beta-propeller, TolB-like (1);	0.335734	0.30501	N	0.009486	T	0.69387	0.3105	M	0.80746	2.51	0.27421	N	0.954286	D	0.76494	0.999	D	0.78314	0.991	T	0.62134	-0.6918	10	0.87932	D	0	-4.9952	8.5503	0.33447	0.0:0.8963:0.0:0.1037	.	11	P27169	PON1_HUMAN	W	11	ENSP00000222381:G11W	ENSP00000222381:G11W	G	-	1	0	PON1	94791693	0.849000	0.29639	0.207000	0.23584	0.072000	0.16883	1.882000	0.39648	1.413000	0.46997	0.555000	0.69702	GGG		0.607	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
TRRAP	8295	broad.mit.edu	37	7	98580929	98580935	+	Frame_Shift_Del	DEL	AACGCAG	AACGCAG	-	rs537483764		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:98580929_98580935delAACGCAG	ENST00000359863.4	+	59	9057_9063	c.8848_8854delAACGCAG	c.(8848-8856)aacgcaggcfs	p.NAG2950fs	TRRAP_ENST00000355540.3_Frame_Shift_Del_p.NAG2932fs|TRRAP_ENST00000446306.3_Frame_Shift_Del_p.NAG2932fs	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2950	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGCACAAATCAACGCAGGCTTACAGCC	0.522																																						uc003upp.2																			0				ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37						c.(8848-8856)AACGCAGGCfs		transformation/transcription domain-associated																																				SO:0001589	frameshift_variant	8295				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity	g.chr7:98580929_98580935delAACGCAG	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8848_8854delAACGCAG	7.37:g.98580929_98580935delAACGCAG	ENSP00000352925:p.Asn2950fs					TRRAP_uc011kis.1_Frame_Shift_Del_p.N2932fs|TRRAP_uc003upr.2_Frame_Shift_Del_p.N2649fs	p.N2950fs	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	STAD - Stomach adenocarcinoma(171;0.215)		59	9057_9063	+	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		2950_2952			FAT.		A4D265|O75218|Q9Y631|Q9Y6H4	Frame_Shift_Del	DEL	ENST00000359863.4	37	c.8848_8854delAACGCAG	CCDS59066.1																																																																																				0.522	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
PIK3CG	5294	broad.mit.edu	37	7	106513286	106513286	+	Silent	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:106513286C>T	ENST00000359195.3	+	4	2500	c.2190C>T	c.(2188-2190)caC>caT	p.H730H	PIK3CG_ENST00000496166.1_Silent_p.H730H|PIK3CG_ENST00000440650.2_Silent_p.H730H	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	730					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CCATGCTGCACGACTTTACCC	0.473																																						uc003vdv.3																			0				lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						c.(2188-2190)CAC>CAT		phosphoinositide-3-kinase, catalytic, gamma							119.0	115.0	117.0					7																	106513286		2203	4300	6503	SO:0001819	synonymous_variant	5294				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding	g.chr7:106513286C>T		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2190C>T	7.37:g.106513286C>T						PIK3CG_uc003vdu.2_Silent_p.H730H|PIK3CG_uc003vdw.2_Silent_p.H730H	p.H730H	NM_002649	NP_002640	P48736	PK3CG_HUMAN			4	2275	+			730					A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	c.2190C>T	CCDS5739.1																																																																																				0.473	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
AKR1B15	441282	broad.mit.edu	37	7	134260192	134260192	+	Silent	SNP	C	C	T	rs4035285		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:134260192C>T	ENST00000457545.2	+	7	794	c.534C>T	c.(532-534)gaC>gaT	p.D178D	AKR1B15_ENST00000423958.1_Silent_p.D150D	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	178							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						AGCTGGTGGACGAGGGGCTGG	0.517																																						uc011kpr.1																			0				ovary(1)	1						c.(532-534)GAC>GAT		aldo-keto reductase family 1, member B15							61.0	64.0	63.0					7																	134260192		2203	4300	6503	SO:0001819	synonymous_variant	441282						oxidoreductase activity	g.chr7:134260192C>T		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.534C>T	7.37:g.134260192C>T						AKR1B15_uc011kps.1_Silent_p.D150D	p.D178D	NM_001080538	NP_001074007	C9JRZ8	AK1BF_HUMAN			7	833	+			178					C9J3V2	Silent	SNP	ENST00000457545.2	37	c.534C>T	CCDS47715.2																																																																																				0.517	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
KMT2C	58508	broad.mit.edu	37	7	151877846	151877846	+	Missense_Mutation	SNP	T	T	C			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr7:151877846T>C	ENST00000262189.6	-	36	7317	c.7099A>G	c.(7099-7101)Aca>Gca	p.T2367A	KMT2C_ENST00000355193.2_Missense_Mutation_p.T2367A	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2367					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GTATTCTGTGTATCAGTTACT	0.428																																						uc003wla.2										N							medulloblastoma		0				large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63						c.(7099-7101)ACA>GCA		myeloid/lymphoid or mixed-lineage leukemia 3							77.0	73.0	75.0					7																	151877846		2203	4300	6503	SO:0001583	missense	58508				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding	g.chr7:151877846T>C	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.7099A>G	7.37:g.151877846T>C	ENSP00000262189:p.Thr2367Ala					MLL3_uc003wkz.2_Missense_Mutation_p.T1428A|MLL3_uc003wky.2_5'Flank	p.T2367A	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)	36	7318	-	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	2367					Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	c.7099A>G	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336467	0.24253	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.82433	-1.61;-1.6	5.11	3.96	0.45880	.	0.304193	0.22950	N	0.053676	T	0.74635	0.3742	L	0.57536	1.79	0.46654	D	0.999149	P;P	0.46859	0.469;0.885	B;B	0.40066	0.185;0.318	T	0.70270	-0.4918	10	0.08599	T	0.76	.	8.0787	0.30731	0.0:0.1558:0.0:0.8442	.	2367;1428	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	A	2367	ENSP00000262189:T2367A;ENSP00000347325:T2367A	ENSP00000262189:T2367A	T	-	1	0	MLL3	151508779	0.901000	0.30685	0.108000	0.21378	0.691000	0.40173	1.165000	0.31822	0.908000	0.36671	0.528000	0.53228	ACA		0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MROH5	389690	broad.mit.edu	37	8	142476586	142476586	+	RNA	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr8:142476586G>A	ENST00000430863.1	-	0	2480					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GGGTGATGGCGTGCAGGGTCT	0.632																																						uc003ywi.2																			0					0						c.(2398-2400)CAC>CAT		hypothetical protein LOC389690							72.0	85.0	81.0					8																	142476586		2147	4237	6384			389690						binding	g.chr8:142476586G>A			8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142476586G>A						FLJ43860_uc011ljs.1_RNA|FLJ43860_uc010meu.1_RNA	p.H800H	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0493)		19	2481	-	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		800						Silent	SNP	ENST00000430863.1	37	c.2400C>T																																																																																					0.632	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414	
HSF1	3297	broad.mit.edu	37	8	145537533	145537533	+	Missense_Mutation	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr8:145537533C>T	ENST00000528838.1	+	11	1433	c.1273C>T	c.(1273-1275)Ccc>Tcc	p.P425S	HSF1_ENST00000400780.4_Intron|HSF1_ENST00000528842.1_3'UTR|DGAT1_ENST00000527438.1_5'Flank|GS1-393G12.12_ENST00000525023.1_RNA	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1	425	Transactivation domain.				cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			GGTGACCGTGCCCGACATGAG	0.716																																						uc003zbt.3																			0					0						c.(1273-1275)CCC>TCC		heat shock transcription factor 1							44.0	47.0	46.0					8																	145537533		2201	4297	6498	SO:0001583	missense	3297					cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity	g.chr8:145537533C>T	M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604	ENST00000528838.1:c.1273C>T	8.37:g.145537533C>T	ENSP00000431512:p.Pro425Ser					HSF1_uc003zbu.3_RNA	p.P425S	NM_005526	NP_005517	Q00613	HSF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)		11	1443	+	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		425			Transactivation domain.		A8K4L0|A8MW26|Q53XT4	Missense_Mutation	SNP	ENST00000528838.1	37	c.1273C>T	CCDS6419.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.930755	0.00488	.	.	ENSG00000185122	ENST00000528838	.	.	.	4.75	2.76	0.32466	Vertebrate heat shock transcription factor (1);	0.592725	0.16725	N	0.202102	T	0.19765	0.0475	N	0.04959	-0.14	0.20196	N	0.999927	B	0.18310	0.027	B	0.23419	0.046	T	0.18429	-1.0337	9	0.07175	T	0.84	-17.0638	11.439	0.50086	0.3362:0.6638:0.0:0.0	.	425	Q00613	HSF1_HUMAN	S	425	.	ENSP00000431512:P425S	P	+	1	0	HSF1	145508341	0.527000	0.26306	0.037000	0.18230	0.003000	0.03518	1.173000	0.31920	1.200000	0.43188	-0.188000	0.12872	CCC		0.716	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382053.1	NM_005526	
EXD3	54932	broad.mit.edu	37	9	140201615	140201615	+	Silent	SNP	G	G	A	rs558615597		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chr9:140201615G>A	ENST00000340951.4	-	22	2613	c.2418C>T	c.(2416-2418)gcC>gcT	p.A806A	EXD3_ENST00000342129.4_Silent_p.A444A	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GGGTGCCGTCGGCCAGCATGT	0.697																																						uc004cmp.2																			0					0						c.(2416-2418)GCC>GCT		exonuclease 3'-5' domain containing 3							10.0	13.0	12.0					9																	140201615		1995	4163	6158	SO:0001819	synonymous_variant	54932				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding	g.chr9:140201615G>A		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.2418C>T	9.37:g.140201615G>A						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Silent_p.A444A	p.A806A	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN			22	2614	-			806					Q6P1M1|Q8IXT8	Silent	SNP	ENST00000340951.4	37	c.2418C>T	CCDS48066.1																																																																																				0.697	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
MAGEB4	4115	broad.mit.edu	37	X	30260469	30260469	+	Missense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chrX:30260469G>A	ENST00000378982.2	+	1	413	c.217G>A	c.(217-219)Gca>Aca	p.A73T	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	73										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CTCTGCTGCTGCAGCTATGTC	0.527																																						uc004dcb.2																			0				ovary(1)	1						c.(217-219)GCA>ACA		melanoma antigen family B, 4							53.0	47.0	49.0					X																	30260469		2202	4300	6502	SO:0001583	missense	4115							g.chrX:30260469G>A		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"""melanoma-associated antigen B4"", ""cancer/testis antigen family 3, member 6"""	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.217G>A	X.37:g.30260469G>A	ENSP00000368266:p.Ala73Thr					MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	p.A73T	NM_002367	NP_002358	O15481	MAGB4_HUMAN			1	301	+			73					B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	37	c.217G>A	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307716	0.40795	.	.	ENSG00000120289	ENST00000378982	T	0.05786	3.39	3.24	-0.712	0.11226	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.18130	0.0435	M	0.80028	2.48	0.09310	N	1	D	0.63880	0.993	D	0.70016	0.967	T	0.10753	-1.0616	9	0.49607	T	0.09	.	2.5936	0.04848	0.4195:0.0:0.3592:0.2213	.	73	O15481	MAGB4_HUMAN	T	73	ENSP00000368266:A73T	ENSP00000368266:A73T	A	+	1	0	MAGEB4	30170390	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.037000	0.13840	-0.317000	0.08677	0.544000	0.68410	GCA		0.527	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367	
CCDC120	90060	broad.mit.edu	37	X	48923077	48923077	+	Missense_Mutation	SNP	C	C	T	rs148446381		TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chrX:48923077C>T	ENST00000376396.3	+	8	994	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W	CCDC120_ENST00000422185.2_Missense_Mutation_p.R259W|CCDC120_ENST00000496529.2_Missense_Mutation_p.R259W|CCDC120_ENST00000597275.1_Missense_Mutation_p.R259W|CCDC120_ENST00000603986.1_Missense_Mutation_p.R294W|CCDC120_ENST00000536628.2_Missense_Mutation_p.R247W	NM_001271835.1|NM_001271836.1|NM_033626.2	NP_001258764.1|NP_001258765.1|NP_296375.1	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	259										breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						GAGCCCTGAGCGGCGAACCCC	0.642																																						uc010nik.2																			0				pancreas(1)	1						c.(775-777)CGG>TGG		coiled-coil domain containing 120 isoform 3		C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,3834		0,0,1632,570	20.0	19.0	19.0		775,739,739,775	3.3	1.0	X	dbSNP_134	19	1,6725		0,1,2427,1870	yes	missense,missense,missense,missense	CCDC120	NM_001163321.1,NM_001163322.1,NM_001163323.1,NM_033626.2	101,101,101,101	0,1,4059,2440	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging	259/662,247/650,247/619,259/631	48923077	1,10559	2202	4298	6500	SO:0001583	missense	90060						protein binding	g.chrX:48923077C>T	BC008769	CCDS14316.1, CCDS55413.1, CCDS55414.1, CCDS55414.2	Xp11.23	2008-02-05			ENSG00000147144	ENSG00000147144			28910	protein-coding gene	gene with protein product						12477932	Standard	NM_033626		Approved	JM11	uc011mmr.3	Q96HB5	OTTHUMG00000021509	ENST00000376396.3:c.775C>T	X.37:g.48923077C>T	ENSP00000365577:p.Arg259Trp					CCDC120_uc011mmq.1_Missense_Mutation_p.R247W|CCDC120_uc004dmf.2_Missense_Mutation_p.R259W|CCDC120_uc010nil.2_Missense_Mutation_p.R259W|CCDC120_uc011mmr.1_Missense_Mutation_p.R259W|CCDC120_uc011mms.1_Missense_Mutation_p.R247W	p.R259W	NM_033626	NP_296375	Q96HB5	CC120_HUMAN			8	1282	+			259					B4DFC1|B4DTU2|F5GZU4	Missense_Mutation	SNP	ENST00000376396.3	37	c.775C>T	CCDS14316.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.876104	0.72180	0.0	1.49E-4	ENSG00000147144	ENST00000376396;ENST00000422185;ENST00000536628	.	.	.	5.15	3.29	0.37713	.	0.122796	0.56097	D	0.000032	T	0.67683	0.2919	L	0.50333	1.59	0.35168	D	0.771298	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.74348	0.982;0.983;0.983;0.983	T	0.74725	-0.3568	9	0.72032	D	0.01	-7.1831	10.9112	0.47110	0.341:0.659:0.0:0.0	.	247;294;247;259	B4DTU2;B4DFC1;B4DF24;Q96HB5	.;.;.;CC120_HUMAN	W	259;259;247	.	ENSP00000365577:R259W	R	+	1	2	CCDC120	48810021	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	1.936000	0.40183	0.444000	0.26612	0.529000	0.55759	CGG		0.642	CCDC120-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056528.1	NM_033626	
BRWD3	254065	broad.mit.edu	37	X	79938109	79938109	+	Nonsense_Mutation	SNP	G	G	A			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chrX:79938109G>A	ENST00000373275.4	-	38	4468	c.4252C>T	c.(4252-4254)Cga>Tga	p.R1418*	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1418					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						GCAGATAATCGCAGCATCATG	0.338																																						uc004edt.2																			0				ovary(4)	4						c.(4252-4254)CGA>TGA		bromodomain and WD repeat domain containing 3							120.0	103.0	109.0					X																	79938109		2203	4300	6503	SO:0001587	stop_gained	254065							g.chrX:79938109G>A		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4252C>T	X.37:g.79938109G>A	ENSP00000362372:p.Arg1418*					BRWD3_uc010nmi.1_RNA|BRWD3_uc004edo.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edp.2_Nonsense_Mutation_p.R1247*|BRWD3_uc004edq.2_Nonsense_Mutation_p.R1014*|BRWD3_uc010nmj.1_Nonsense_Mutation_p.R1014*|BRWD3_uc004edr.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eds.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edu.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004edv.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edw.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edx.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edy.2_Nonsense_Mutation_p.R1014*|BRWD3_uc004edz.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eea.2_Nonsense_Mutation_p.R1088*|BRWD3_uc004eeb.2_Nonsense_Mutation_p.R1014*	p.R1418*	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN			38	4515	-			1418					C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Nonsense_Mutation	SNP	ENST00000373275.4	37	c.4252C>T	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	44	11.030795	0.99505	.	.	ENSG00000165288	ENST00000373275	.	.	.	4.82	2.96	0.34315	.	0.112670	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.2934	12.6899	0.56968	0.0:0.0:0.6934:0.3066	.	.	.	.	X	1418	.	.	R	-	1	2	BRWD3	79824765	0.989000	0.36119	0.998000	0.56505	0.811000	0.45836	0.563000	0.23547	0.404000	0.25506	0.415000	0.27848	CGA		0.338	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
NXF3	56000	broad.mit.edu	37	X	102334798	102334798	+	Splice_Site	SNP	C	C	T			TCGA-27-1833-01A-01W-0643-08	TCGA-27-1833-10A-01W-0644-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	4d8d34d9-7069-436c-84d6-ace5760c2aec	f8e118cf-6937-4ff5-a3d2-77fb32519488	g.chrX:102334798C>T	ENST00000395065.3	-	13	1154	c.1053G>A	c.(1051-1053)caG>caA	p.Q351Q	NXF3_ENST00000425644.1_Splice_Site_p.R23R	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	351	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						TCAAGTAATACCTGTTGGAGA	0.493																																						uc004eju.2																			0				ovary(1)|lung(1)|central_nervous_system(1)	3						c.(1051-1053)CAG>CAA		nuclear RNA export factor 3							113.0	101.0	105.0					X																	102334798		2203	4300	6503	SO:0001630	splice_region_variant	56000					cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding	g.chrX:102334798C>T	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1053-1G>A	X.37:g.102334798C>T						NXF3_uc010noi.1_Silent_p.Q201Q	p.Q351Q	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN			13	1124	-			351			NTF2.		B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	37	c.1053G>A	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.240053	0.22711	.	.	ENSG00000147206	ENST00000427570	.	.	.	4.44	-2.31	0.06765	.	.	.	.	.	T	0.39545	0.1082	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24870	-1.0148	4	.	.	.	.	2.1205	0.03724	0.1254:0.4378:0.1213:0.3156	.	.	.	.	I	228	.	.	V	-	1	0	NXF3	102221454	1.000000	0.71417	0.233000	0.24025	0.865000	0.49528	1.081000	0.30791	-0.882000	0.03987	0.600000	0.82982	GTA		0.493	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052	Silent
