#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
FAT3	120114	broad.mit.edu	37	11	92568131	92568131	+	Missense_Mutation	SNP	G	G	A	rs572769099		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr11:92568131G>A	ENST00000298047.6	+	14	9984	c.9967G>A	c.(9967-9969)Gct>Act	p.A3323T	FAT3_ENST00000409404.2_Missense_Mutation_p.A3323T|FAT3_ENST00000525166.1_Missense_Mutation_p.A3173T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3323	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A3323T(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGCTCTCAGCGCTGTGGCCAC	0.498										TCGA Ovarian(4;0.039)			G|||	1	0.000199681	0.0	0.0	5008	,	,		16658	0.0		0.0	False		,,,				2504	0.001					ENST00000298047.6																			2	Substitution - Missense(2)	p.A3323T(2)	prostate(2)	NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85						c.(9967-9969)Gct>Act		FAT atypical cadherin 3							45.0	46.0	46.0					11																	92568131		1945	4139	6084	SO:0001583	missense	120114				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	g.chr11:92568131G>A	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9967G>A	11.37:g.92568131G>A	ENSP00000298047:p.Ala3323Thr	TCGA Ovarian(4;0.039)				FAT3_ENST00000525166.1_Missense_Mutation_p.A3173T|FAT3_ENST00000409404.2_Missense_Mutation_p.A3323T	p.A3323T			Q8TDW7	FAT3_HUMAN			14	9984	+		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)	3323			Cadherin 30.		B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37	c.9967G>A		.	.	.	.	.	.	.	.	.	.	G	14.72	2.618557	0.46736	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.03181	4.02;4.02;4.02	5.46	3.56	0.40772	.	.	.	.	.	T	0.03136	0.0092	N	0.21448	0.665	0.80722	D	1	B	0.19817	0.039	B	0.15870	0.014	T	0.49934	-0.8886	9	0.41790	T	0.15	.	9.8021	0.40770	0.0736:0.0:0.7862:0.1402	.	3323	Q8TDW7-3	.	T	3323;3323;3173	ENSP00000298047:A3323T;ENSP00000387040:A3323T;ENSP00000432586:A3173T	ENSP00000298047:A3323T	A	+	1	0	FAT3	92207779	1.000000	0.71417	0.072000	0.20136	0.900000	0.52787	4.843000	0.62838	0.630000	0.30394	0.655000	0.94253	GCT		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		17	17	0	0	0	0.500413	0	17	17				
SUCO	51430	broad.mit.edu	37	1	172501831	172501831	+	5'Flank	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:172501831C>T	ENST00000263688.3	+	0	0				SUCO_ENST00000367723.4_Silent_p.N73N|SUCO_ENST00000610051.1_5'Flank|SUCO_ENST00000608151.1_Silent_p.N73N	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor						multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)		p.N73N(1)									ACTTCTCTAACAAAACCATGG	0.498																																						ENST00000367723.3																			1	Substitution - coding silent(1)	p.N73N(1)	prostate(1)								c.(217-219)aaC>aaT		SUN domain containing ossification factor							77.0	77.0	77.0					1																	172501831		1890	4118	6008	SO:0001631	upstream_gene_variant	51430							g.chr1:172501831C>T	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839		1.37:g.172501831C>T	Exception_encountered						p.N73N	NM_016227.2	NP_057311.2					1	343	+								B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	c.219C>T	CCDS1303.1																																																																																				0.498	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		6	78	0	0	0	0.248553	0	6	78				
ATP6V1A	523	broad.mit.edu	37	3	113508598	113508598	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:113508598G>T	ENST00000273398.3	+	8	1007	c.899G>T	c.(898-900)gGt>gTt	p.G300V	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.G267V	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	300					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.G300V(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GAGGTTGATGGTAAGGTAGAG	0.353																																						ENST00000273398.3																			1	Substitution - Missense(1)	p.G300V(1)	prostate(1)	breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						c.(898-900)gGt>gTt		ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A							91.0	91.0	91.0					3																	113508598		2203	4300	6503	SO:0001583	missense	523				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism	g.chr3:113508598G>T	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.899G>T	3.37:g.113508598G>T	ENSP00000273398:p.Gly300Val					ATP6V1A_ENST00000538620.1_Missense_Mutation_p.G267V	p.G300V	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN			8	1007	+			300					B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	c.899G>T	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257803	0.80246	.	.	ENSG00000114573	ENST00000545842;ENST00000273398;ENST00000538620	D;D	0.89617	-2.54;-1.75	5.73	4.86	0.63082	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.046405	0.85682	D	0.000000	D	0.95822	0.8640	H	0.94658	3.565	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.96750	0.9553	10	0.87932	D	0	-17.8735	14.1382	0.65300	0.0725:0.0:0.9275:0.0	.	300	P38606	VATA_HUMAN	V	17;300;267	ENSP00000273398:G300V;ENSP00000439874:G267V	ENSP00000273398:G300V	G	+	2	0	ATP6V1A	114991288	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.149000	0.94659	1.428000	0.47296	0.557000	0.71058	GGT		0.353	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		51	103	1	0	8.04919e-23	0.870114	1.03334e-22	51	103				
ST18	9705	broad.mit.edu	37	8	53045685	53045685	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:53045685G>A	ENST00000276480.7	-	21	3059	c.2376C>T	c.(2374-2376)tgC>tgT	p.C792C		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	792					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.C792C(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGCACGAGGGCATCCGGACA	0.468																																						ENST00000276480.7																			1	Substitution - coding silent(1)	p.C792C(1)	prostate(1)	NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85						c.(2374-2376)tgC>tgT		suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)							119.0	115.0	117.0					8																	53045685		2203	4300	6503	SO:0001819	synonymous_variant	9705					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr8:53045685G>A	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2376C>T	8.37:g.53045685G>A							p.C792C	NM_014682.2	NP_055497.1	O60284	ST18_HUMAN			21	3059	-		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)	792					Q17RY1	Silent	SNP	ENST00000276480.7	37	c.2376C>T	CCDS6149.1																																																																																				0.468	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			4	233	0	0	0	0.150653	0	4	233				
COL6A5	256076	broad.mit.edu	37	3	130159274	130159274	+	Missense_Mutation	SNP	A	A	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:130159274A>T	ENST00000432398.2	+	35	6586	c.6092A>T	c.(6091-6093)gAt>gTt	p.D2031V	COL6A5_ENST00000265379.6_Missense_Mutation_p.D2031V	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2031	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.D70V(1)|p.D2031V(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACAGAGTTTGATTTCATCACT	0.423																																						ENST00000265379.6																			2	Substitution - Missense(2)	p.D70V(1)|p.D2031V(1)	prostate(2)	endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						c.(6091-6093)gAt>gTt		collagen, type VI, alpha 5							95.0	90.0	92.0					3																	130159274		1888	4107	5995	SO:0001583	missense	256076				axon guidance|cell adhesion	collagen		g.chr3:130159274A>T	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6092A>T	3.37:g.130159274A>T	ENSP00000390895:p.Asp2031Val					COL6A5_ENST00000432398.2_Missense_Mutation_p.D2031V	p.D2031V			A8TX70	CO6A5_HUMAN			35	6586	+			2031			Nonhelical region.|VWFA 9.		A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37	c.6092A>T		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.217|3.217	-0.160309|-0.160309	0.06502|0.06502	.|.	.|.	ENSG00000172752|ENSG00000172752	ENST00000432398;ENST00000265379|ENST00000512836	T;T|.	0.16457|.	2.34;2.34|.	5.76|5.76	-3.64|-3.64	0.04515|0.04515	von Willebrand factor, type A (3);|.	1.257190|.	0.05679|.	N|.	0.590065|.	T|.	0.32071|.	0.0817|.	L|L	0.47190|0.47190	1.495|1.495	0.24250|0.24250	N|N	0.995324|0.995324	B;B|.	0.30068|.	0.267;0.225|.	B;B|.	0.27380|.	0.079;0.047|.	T|.	0.36986|.	-0.9725|.	10|.	0.28530|.	T|.	0.3|.	.|.	3.0106|3.0106	0.06043|0.06043	0.3959:0.3673:0.1296:0.1072|0.3959:0.3673:0.1296:0.1072	.|.	2031;2031|.	A8TX70;A8TX70-2|.	CO6A5_HUMAN;.|.	V|C	2031|282	ENSP00000390895:D2031V;ENSP00000265379:D2031V|.	ENSP00000265379:D2031V|.	D|X	+|+	2|3	0|0	COL6A5|COL6A5	131641964|131641964	0.029000|0.029000	0.19370|0.19370	0.010000|0.010000	0.14722|0.14722	0.293000|0.293000	0.27360|0.27360	0.282000|0.282000	0.18829|0.18829	-0.443000|-0.443000	0.07180|0.07180	-0.313000|-0.313000	0.08912|0.08912	GAT|TGA		0.423	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		45	100	0	0	0	0.859065	0	45	100				
MATN4	8785	broad.mit.edu	37	20	43926838	43926838	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:43926838C>T	ENST00000372754.1	-	7	1529	c.1521G>A	c.(1519-1521)tcG>tcA	p.S507S	MATN4_ENST00000360607.6_Silent_p.S425S|MATN4_ENST00000372751.4_Silent_p.S317S|MATN4_ENST00000372756.1_Silent_p.S466S|MATN4_ENST00000537548.1_Silent_p.S466S|MATN4_ENST00000342716.4_Silent_p.S466S|MATN4_ENST00000353917.5_Silent_p.S384S			O95460	MATN4_HUMAN	matrilin 4	507	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)		p.S466S(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CTGCCCACACCGAGATGTCAT	0.672																																						ENST00000537548.1																			1	Substitution - coding silent(1)	p.S466S(1)	prostate(1)	central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						c.(1396-1398)tcG>tcA		matrilin 4							55.0	48.0	51.0					20																	43926838		2203	4300	6503	SO:0001819	synonymous_variant	8785					extracellular region	protein binding	g.chr20:43926838C>T	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1521G>A	20.37:g.43926838C>T						MATN4_ENST00000342716.4_Silent_p.S466S|MATN4_ENST00000372754.1_Silent_p.S507S|MATN4_ENST00000372753.1_Silent_p.S317S|MATN4_ENST00000372756.1_Silent_p.S466S|MATN4_ENST00000372751.4_Silent_p.S317S|MATN4_ENST00000360607.5_Silent_p.S425S|MATN4_ENST00000353917.5_Silent_p.S384S	p.S466S			O95460	MATN4_HUMAN			8	1642	-		Myeloproliferative disorder(115;0.0122)	507			VWFA 2.		A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37	c.1398G>A																																																																																					0.672	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			5	73	0	0	0	0.217242	0	5	73				
TXNIP	10628	broad.mit.edu	37	1	145440347	145440347	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:145440347G>T	ENST00000369317.4	+	5	987	c.653G>T	c.(652-654)cGc>cTc	p.R218L	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	218					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)	p.R218L(1)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATTGTGGCCCGCCACACTTAC	0.478																																						ENST00000369317.4																			1	Substitution - Missense(1)	p.R218L(1)	prostate(1)	breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21						c.(652-654)cGc>cTc		thioredoxin interacting protein							88.0	87.0	87.0					1																	145440347		2203	4300	6503	SO:0001583	missense	10628				cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding	g.chr1:145440347G>T	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"""upregulated by 1,25-dihydroxyvitamin D-3"", ""thioredoxin binding protein 2"""	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.653G>T	1.37:g.145440347G>T	ENSP00000358323:p.Arg218Leu					TXNIP_ENST00000475171.1_Intron	p.R218L	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN			5	987	+	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		218					B4E3D3|Q16226|Q6PML0|Q9BXG9	Missense_Mutation	SNP	ENST00000369317.4	37	c.653G>T	CCDS913.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100742	0.56183	.	.	ENSG00000117289	ENST00000369317;ENST00000425134	T;T	0.19394	2.15;2.15	5.69	5.69	0.88448	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.129021	0.53938	D	0.000056	T	0.05777	0.0151	N	0.22421	0.69	0.40344	D	0.979063	B;B	0.33857	0.429;0.3	B;B	0.34489	0.184;0.07	T	0.20207	-1.0282	10	0.11794	T	0.64	-12.8536	10.7119	0.45988	0.0864:0.0:0.9136:0.0	.	163;218	B4E3D3;Q9H3M7	.;TXNIP_HUMAN	L	218;163	ENSP00000358323:R218L;ENSP00000396322:R163L	ENSP00000358323:R218L	R	+	2	0	TXNIP	144151704	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	4.007000	0.57093	2.696000	0.92011	0.651000	0.88453	CGC		0.478	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		21	118	1	0	9.95505e-16	0.624587	1.22822e-15	21	118				
VIPAS39	63894	broad.mit.edu	37	14	77896064	77896064	+	Missense_Mutation	SNP	C	C	T	rs200598365		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:77896064C>T	ENST00000553888.1	-	17	1736	c.1226G>A	c.(1225-1227)cGg>cAg	p.R409Q	VIPAS39_ENST00000557658.1_Missense_Mutation_p.R409Q|VIPAS39_ENST00000327028.4_Missense_Mutation_p.R396Q|VIPAS39_ENST00000343765.2_Missense_Mutation_p.R409Q|VIPAS39_ENST00000448935.2_Missense_Mutation_p.R360Q|VIPAS39_ENST00000556412.1_Missense_Mutation_p.R435Q	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2	Q9H9C1	SPE39_HUMAN	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	409					cell differentiation (GO:0030154)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|late endosome (GO:0005770)|recycling endosome (GO:0055037)		p.R409Q(1)									TTCGACAACCCGATGGAAGCC	0.502																																						ENST00000553888.1																			1	Substitution - Missense(1)	p.R409Q(1)	prostate(1)								c.(1225-1227)cGg>cAg		VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog							215.0	202.0	206.0					14																	77896064		2203	4300	6503	SO:0001583	missense	63894							g.chr14:77896064C>T	AK022925	CCDS9862.1, CCDS53905.1	14q24.3-q31	2013-08-14	2012-07-24	2012-07-24	ENSG00000151445	ENSG00000151445			20347	protein-coding gene	gene with protein product	"""VPS33B interacting protein, apical-basolateral polarity regulator"""	613401	"""chromosome 14 open reading frame 133"""	C14orf133		20190753, 19109425, 22753090, 23002115, 23918659	Standard	NM_022067		Approved	VIPAR, VPS16B, SPE-39, SPE39, hSPE-39	uc001xtu.2	Q9H9C1		ENST00000553888.1:c.1226G>A	14.37:g.77896064C>T	ENSP00000452181:p.Arg409Gln					VIPAS39_ENST00000448935.2_Missense_Mutation_p.R360Q|VIPAS39_ENST00000327028.4_Missense_Mutation_p.R396Q|VIPAS39_ENST00000343765.2_Missense_Mutation_p.R409Q|VIPAS39_ENST00000557658.1_Missense_Mutation_p.R409Q|VIPAS39_ENST00000556412.1_Missense_Mutation_p.R435Q	p.R409Q	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2					17	1736	-								B4DPI6|O95434|Q9H7E1|Q9H9I9	Missense_Mutation	SNP	ENST00000553888.1	37	c.1226G>A	CCDS9862.1	.	.	.	.	.	.	.	.	.	.	C	36	5.648077	0.96714	.	.	ENSG00000151445	ENST00000343765;ENST00000553888;ENST00000327028;ENST00000557658;ENST00000448935;ENST00000556412	T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.61185	0.2327	M	0.66939	2.045	0.80722	D	1	P;D	0.54601	0.922;0.967	B;P	0.49665	0.429;0.618	T	0.58509	-0.7624	10	0.28530	T	0.3	-12.1488	18.2507	0.90002	0.0:1.0:0.0:0.0	.	360;409	B4DPI6;Q9H9C1	.;VIPAR_HUMAN	Q	409;409;396;409;360;435	ENSP00000339122:R409Q;ENSP00000452181:R409Q;ENSP00000313098:R396Q;ENSP00000452191:R409Q;ENSP00000404815:R360Q;ENSP00000451857:R435Q	ENSP00000313098:R396Q	R	-	2	0	VIPAR	76965817	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.286000	0.78671	2.608000	0.88229	0.655000	0.94253	CGG		0.502	VIPAS39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414008.1	NM_022067		25	414	0	0	0	0.667858	0	25	414				
LHX5	64211	broad.mit.edu	37	12	113909233	113909233	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:113909233G>A	ENST00000261731.3	-	1	644	c.71C>T	c.(70-72)gCg>gTg	p.A24V	LHX5_ENST00000557836.1_5'Flank|RP11-82C23.2_ENST00000551357.2_RNA	NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	24	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.A24V(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						GATGTGCCACGCGCGGTCCAG	0.612																																						ENST00000261731.3																			1	Substitution - Missense(1)	p.A24V(1)	prostate(1)	NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						c.(70-72)gCg>gTg		LIM homeobox 5							43.0	34.0	37.0					12																	113909233		2203	4300	6503	SO:0001583	missense	64211					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr12:113909233G>A	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"""Homeoboxes / LIM class"""	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.71C>T	12.37:g.113909233G>A	ENSP00000261731:p.Ala24Val						p.A24V	NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN			1	644	-			24			LIM zinc-binding 1.		Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	37	c.71C>T	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	G	33	5.215834	0.95104	.	.	ENSG00000089116	ENST00000261731	D	0.86956	-2.19	4.04	4.04	0.47022	Zinc finger, LIM-type (5);	0.000000	0.48767	D	0.000163	D	0.84028	0.5382	L	0.31845	0.965	0.80722	D	1	P	0.44344	0.833	P	0.47162	0.54	T	0.81682	-0.0822	10	0.20519	T	0.43	.	16.3982	0.83630	0.0:0.0:1.0:0.0	.	24	Q9H2C1	LHX5_HUMAN	V	24	ENSP00000261731:A24V	ENSP00000261731:A24V	A	-	2	0	LHX5	112393616	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.783000	0.85696	2.084000	0.62774	0.491000	0.48974	GCG		0.612	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		3	16	0	0	0	0.115264	0	3	16				
CROT	54677	broad.mit.edu	37	7	86990868	86990868	+	Missense_Mutation	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:86990868T>A	ENST00000331536.3	+	5	588	c.403T>A	c.(403-405)Tac>Aac	p.Y135N	CROT_ENST00000442291.1_Missense_Mutation_p.Y135N|CROT_ENST00000419147.2_Missense_Mutation_p.Y163N	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	135					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)	p.Y135N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TAACTTGAACTACTGGCAGCT	0.398																																						ENST00000331536.3																			1	Substitution - Missense(1)	p.Y135N(1)	prostate(1)	NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						c.(403-405)Tac>Aac		carnitine O-octanoyltransferase	L-Carnitine(DB00583)						79.0	77.0	78.0					7																	86990868		2203	4300	6503	SO:0001583	missense	54677				fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity	g.chr7:86990868T>A		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.403T>A	7.37:g.86990868T>A	ENSP00000331981:p.Tyr135Asn					CROT_ENST00000442291.1_Missense_Mutation_p.Y135N|CROT_ENST00000419147.2_Missense_Mutation_p.Y163N	p.Y135N	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN			5	588	+	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)		135					A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	c.403T>A	CCDS5604.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360649	0.82353	.	.	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.90385	-2.66;-2.66;-2.66	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.85130	0.949;0.997	D	0.97564	1.0100	10	0.87932	D	0	-8.6824	16.2669	0.82588	0.0:0.0:0.0:1.0	.	163;135	E7EQF2;Q9UKG9	.;OCTC_HUMAN	N	163;135;135	ENSP00000413575:Y163N;ENSP00000331981:Y135N;ENSP00000411983:Y135N	ENSP00000331981:Y135N	Y	+	1	0	CROT	86828804	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.740000	0.84986	2.240000	0.73641	0.533000	0.62120	TAC		0.398	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		6	178	0	0	0	0.217242	0	6	178				
SPATA31A6	389730	broad.mit.edu	37	9	43627187	43627187	+	Silent	SNP	C	C	T	rs561244020	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:43627187C>T	ENST00000332857.6	-	4	1528	c.1500G>A	c.(1498-1500)caG>caA	p.Q500Q	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	500					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.Q500Q(1)									GGAAAGAAGACTGAAGATGGG	0.547													T|||	3	0.000599042	0.0	0.0	5008	,	,		14137	0.0		0.002	False		,,,				2504	0.001					ENST00000332857.6																			1	Substitution - coding silent(1)	p.Q500Q(1)	prostate(1)								c.(1498-1500)caG>caA		SPATA31 subfamily A, member 6							63.0	68.0	66.0					9																	43627187		612	1534	2146	SO:0001819	synonymous_variant	389730							g.chr9:43627187C>T		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.1500G>A	9.37:g.43627187C>T							p.Q500Q	NM_001145196.1	NP_001138668.1					4	1528	-									Silent	SNP	ENST00000332857.6	37	c.1500G>A	CCDS47973.1																																																																																				0.547	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196		6	526	0	0	0	0.217242	0	6	526				
SRMS	6725	broad.mit.edu	37	20	62178595	62178595	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:62178595G>A	ENST00000217188.1	-	1	262	c.222C>T	c.(220-222)cgC>cgT	p.R74R		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	74	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R74R(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GCCTGTCCCCGCGGCGGACAC	0.701																																						ENST00000217188.1																			1	Substitution - coding silent(1)	p.R74R(1)	prostate(1)	breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19						c.(220-222)cgC>cgT		src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites							119.0	123.0	122.0					20																	62178595		2201	4292	6493	SO:0001819	synonymous_variant	6725						ATP binding|non-membrane spanning protein tyrosine kinase activity	g.chr20:62178595G>A		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.222C>T	20.37:g.62178595G>A							p.R74R	NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)		1	262	-	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		74			SH3.			Silent	SNP	ENST00000217188.1	37	c.222C>T	CCDS13525.1																																																																																				0.701	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823		28	359	0	0	0	0.740014	0	28	359				
RYR1	6261	broad.mit.edu	37	19	38976722	38976722	+	Missense_Mutation	SNP	C	C	A	rs201086478		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:38976722C>A	ENST00000359596.3	+	34	5427	c.5427C>A	c.(5425-5427)gaC>gaA	p.D1809E	RYR1_ENST00000360985.3_Missense_Mutation_p.D1809E|RYR1_ENST00000355481.4_Missense_Mutation_p.D1809E			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1809	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.D1809E(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCCTGCGGGACAAGGCACTGA	0.711																																						ENST00000355481.4																			1	Substitution - Missense(1)	p.D1809E(1)	prostate(1)	NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285						c.(5425-5427)gaC>gaA		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)						36.0	38.0	37.0					19																	38976722		2201	4296	6497	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:38976722C>A	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5427C>A	19.37:g.38976722C>A	ENSP00000352608:p.Asp1809Glu					RYR1_ENST00000360985.3_Missense_Mutation_p.D1809E|RYR1_ENST00000359596.3_Missense_Mutation_p.D1809E	p.D1809E	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		34	5558	+	all_cancers(60;7.91e-06)		1809			6 X approximate repeats.		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.5427C>A	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503612	0.44558	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.71461	-0.57;-0.57;-0.57	3.7	-0.0852	0.13687	.	0.724978	0.12030	U	0.506064	T	0.47838	0.1467	N	0.10972	0.075	0.27141	N	0.96164	P;P	0.46220	0.874;0.467	P;B	0.47402	0.546;0.272	T	0.47086	-0.9144	10	0.02654	T	1	.	6.1172	0.20134	0.0:0.5473:0.1413:0.3114	.	1809;1809	P21817-2;P21817	.;RYR1_HUMAN	E	1809	ENSP00000352608:D1809E;ENSP00000347667:D1809E;ENSP00000354254:D1809E	ENSP00000347667:D1809E	D	+	3	2	RYR1	43668562	0.852000	0.29690	0.999000	0.59377	0.942000	0.58702	0.325000	0.19628	0.202000	0.20498	0.585000	0.79938	GAC		0.711	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			43	57	1	0	8.72198e-27	0.870114	1.13505e-26	43	57				
NBN	4683	broad.mit.edu	37	8	90955524	90955524	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:90955524C>A	ENST00000265433.3	-	14	2295	c.2141G>T	c.(2140-2142)cGa>cTa	p.R714L	NBN_ENST00000409330.1_Missense_Mutation_p.R632L	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	714					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)	p.R714L(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGTATTCTTTCGAGCATGATG	0.398								Homologous recombination																														ENST00000265433.3																			1	Substitution - Missense(1)	p.R714L(1)	prostate(1)	autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27						c.(2140-2142)cGa>cTa	Homologous recombination	nibrin							176.0	159.0	164.0					8																	90955524		2203	4300	6503	SO:0001583	missense	4683				cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding	g.chr8:90955524C>A	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.2141G>T	8.37:g.90955524C>A	ENSP00000265433:p.Arg714Leu					NBN_ENST00000409330.1_Missense_Mutation_p.R632L	p.R714L	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	BRCA - Breast invasive adenocarcinoma(11;0.0344)		14	2295	-			714					B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	c.2141G>T	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096879	0.76870	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	T;T	0.61392	0.13;0.11	5.91	3.0	0.34707	DNA repair Nbs1, C-terminal (1);	0.324291	0.35585	N	0.003114	T	0.61961	0.2389	L	0.51422	1.61	0.30998	N	0.720658	D;D	0.54397	0.966;0.966	P;P	0.57152	0.814;0.814	T	0.64761	-0.6331	10	0.72032	D	0.01	-3.6212	8.6164	0.33833	0.0:0.604:0.0:0.396	.	714;714	A6H8Y5;O60934	.;NBN_HUMAN	L	714;632	ENSP00000265433:R714L;ENSP00000386924:R632L	ENSP00000265433:R714L	R	-	2	0	NBN	91024700	0.075000	0.21258	0.987000	0.45799	0.988000	0.76386	0.036000	0.13819	0.335000	0.23614	-0.142000	0.14014	CGA		0.398	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		4	255	1	0	0.014758	0.184627	0.0166906	4	255				
SRSF7	6432	broad.mit.edu	37	2	38976716	38976716	+	Missense_Mutation	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:38976716T>A	ENST00000313117.6	-	3	578	c.341A>T	c.(340-342)cAt>cTt	p.H114L	SRSF7_ENST00000446327.2_Missense_Mutation_p.H114L|GEMIN6_ENST00000409011.1_5'Flank|SRSF7_ENST00000409276.1_Missense_Mutation_p.H114L	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	114					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.H114L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						ATAAGCATAATGTCCCTTTTC	0.413																																						ENST00000313117.6																			1	Substitution - Missense(1)	p.H114L(1)	prostate(1)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(340-342)cAt>cTt		serine/arginine-rich splicing factor 7							158.0	151.0	153.0					2																	38976716		2203	4300	6503	SO:0001583	missense	6432				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding	g.chr2:38976716T>A	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"""Zinc fingers, CCHC domain containing"", ""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10789	protein-coding gene	gene with protein product	"""SR splicing factor 7"""	600572	"""splicing factor, arginine/serine-rich 7 (35kD)"", ""splicing factor, arginine/serine-rich 7, 35kDa"""	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.341A>T	2.37:g.38976716T>A	ENSP00000325905:p.His114Leu					SRSF7_ENST00000409276.1_Missense_Mutation_p.H114L|SRSF7_ENST00000446327.2_Missense_Mutation_p.H114L	p.H114L	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN			3	578	-			114					B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	37	c.341A>T	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.095144	0.76870	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	D;D;D	0.97831	-4.56;-4.56;-4.56	6.03	4.88	0.63580	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2);	0.000000	0.85682	D	0.000000	D	0.98664	0.9552	M	0.87971	2.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99116	1.0848	10	0.87932	D	0	.	11.8765	0.52550	0.0:0.0674:0.0:0.9326	.	114;114	G5E9M3;Q16629	.;SRSF7_HUMAN	L	114	ENSP00000325905:H114L;ENSP00000402264:H114L;ENSP00000386806:H114L	ENSP00000325905:H114L	H	-	2	0	SRSF7	38830220	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.720000	0.84759	1.113000	0.41760	0.533000	0.62120	CAT		0.413	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		27	279	0	0	0	0.729181	0	27	279				
CCDC115	84317	broad.mit.edu	37	2	131096732	131096732	+	Silent	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:131096732G>C	ENST00000259229.2	-	5	727	c.504C>G	c.(502-504)ctC>ctG	p.L168L	CCDC115_ENST00000409127.1_Silent_p.L163L|CCDC115_ENST00000437688.2_3'UTR	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	168						endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)		p.L168L(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7	Colorectal(110;0.1)					GTTTCTCTTGGAGTCCCCGGA	0.612																																						ENST00000259229.2																			1	Substitution - coding silent(1)	p.L168L(1)	prostate(1)	central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7						c.(502-504)ctC>ctG		coiled-coil domain containing 115							63.0	59.0	61.0					2																	131096732		2203	4300	6503	SO:0001819	synonymous_variant	84317					endosome|lysosome		g.chr2:131096732G>C	AK054693	CCDS2159.1	2q21.1	2010-12-24			ENSG00000136710	ENSG00000136710			28178	protein-coding gene	gene with protein product		613734				21118521	Standard	XM_005263825		Approved	MGC12981, FLJ30131, ccp1	uc002tqy.1	Q96NT0	OTTHUMG00000131631	ENST00000259229.2:c.504C>G	2.37:g.131096732G>C						CCDC115_ENST00000409127.1_Silent_p.L163L|CCDC115_ENST00000437688.2_3'UTR	p.L168L	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN			5	727	-	Colorectal(110;0.1)		168					B4DJ47|Q9BR88	Silent	SNP	ENST00000259229.2	37	c.504C>G	CCDS2159.1																																																																																				0.612	CCDC115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254524.2	NM_032357		7	62	0	0	0	0.248553	0	7	62				
TMED9	54732	broad.mit.edu	37	5	177022271	177022271	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:177022271C>T	ENST00000332598.6	+	5	619	c.562C>T	c.(562-564)Cga>Tga	p.R188*		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	188					COPI coating of Golgi vesicle (GO:0048205)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network transport vesicle (GO:0030140)	syntaxin binding (GO:0019905)	p.R188*(1)		endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTGCAGTGGCGAGAGGAGCG	0.602																																						ENST00000332598.6																			1	Substitution - Nonsense(1)	p.R188*(1)	prostate(1)	endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10						c.(562-564)Cga>Tga		transmembrane emp24 protein transport domain containing 9							51.0	48.0	49.0					5																	177022271		2203	4300	6503	SO:0001587	stop_gained	54732				transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane		g.chr5:177022271C>T	AF441399	CCDS4428.1	5q35.3	2008-02-05			ENSG00000184840	ENSG00000184840			24878	protein-coding gene	gene with protein product						12477932	Standard	NM_017510		Approved	HSGP25L2G	uc003mhx.3	Q9BVK6	OTTHUMG00000130859	ENST00000332598.6:c.562C>T	5.37:g.177022271C>T	ENSP00000330945:p.Arg188*						p.R188*	NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		5	619	+	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	188					Q14437|Q8WZ61	Nonsense_Mutation	SNP	ENST00000332598.6	37	c.562C>T	CCDS4428.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.965610	0.92855	.	.	ENSG00000184840	ENST00000332598	.	.	.	5.26	3.38	0.38709	.	0.063886	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.3603	12.2683	0.54691	0.3069:0.6931:0.0:0.0	.	.	.	.	X	188	.	ENSP00000330945:R188X	R	+	1	2	TMED9	176954877	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.850000	0.69473	1.184000	0.42957	0.561000	0.74099	CGA		0.602	TMED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253433.1	NM_017510		29	62	0	0	0	0.740014	0	29	62				
OSER1	51526	broad.mit.edu	37	20	42826279	42826279	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:42826279T>C	ENST00000372970.2	-	6	472	c.292A>G	c.(292-294)Ata>Gta	p.I98V	OSER1_ENST00000255174.2_Missense_Mutation_p.I98V			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	98					cellular response to hydrogen peroxide (GO:0070301)			p.I98V(1)									GAAGACGCTATTGTACTGCAA	0.488																																						ENST00000372970.2																			1	Substitution - Missense(1)	p.I98V(1)	prostate(1)								c.(292-294)Ata>Gta		oxidative stress responsive serine-rich 1							91.0	89.0	90.0					20																	42826279		2203	4300	6503	SO:0001583	missense	51526							g.chr20:42826279T>C	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.292A>G	20.37:g.42826279T>C	ENSP00000362061:p.Ile98Val					OSER1_ENST00000255174.2_Missense_Mutation_p.I98V	p.I98V							6	472	-								B2RCK4|O95912|Q9NZ84|Q9P0R8	Missense_Mutation	SNP	ENST00000372970.2	37	c.292A>G	CCDS13327.1	.	.	.	.	.	.	.	.	.	.	T	0.194	-1.050338	0.01981	.	.	ENSG00000132823	ENST00000255174;ENST00000372970	T;T	0.40756	1.02;1.02	5.58	3.18	0.36537	.	0.570498	0.20465	N	0.091808	T	0.19604	0.0471	N	0.08118	0	0.09310	N	0.999998	B	0.16802	0.019	B	0.19148	0.024	T	0.25984	-1.0116	10	0.10636	T	0.68	-1.4844	8.8311	0.35085	0.1266:0.0:0.1328:0.7405	.	98	Q9NX31	CT111_HUMAN	V	98	ENSP00000255174:I98V;ENSP00000362061:I98V	ENSP00000255174:I98V	I	-	1	0	C20orf111	42259693	0.973000	0.33851	0.993000	0.49108	0.902000	0.53008	1.901000	0.39838	0.418000	0.25898	0.482000	0.46254	ATA		0.488	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470		21	159	0	0	0	0.575678	0	21	159				
PARP2	10038	broad.mit.edu	37	14	20822982	20822982	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:20822982G>A	ENST00000250416.5	+	9	844	c.817G>A	c.(817-819)Gca>Aca	p.A273T	PARP2_ENST00000429687.3_Missense_Mutation_p.A260T|PARP2_ENST00000527915.1_Missense_Mutation_p.A273T	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	273	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A273T(1)|p.A224T(1)		central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GCTGACAGTGGCACAAATCAA	0.468								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																														ENST00000527915.1																			2	Substitution - Missense(2)	p.A273T(1)|p.A224T(1)	kidney(2)	central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15						c.(817-819)Gca>Aca	Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA	poly (ADP-ribose) polymerase 2							129.0	129.0	129.0					14																	20822982		1981	4164	6145	SO:0001583	missense	10038				protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity	g.chr14:20822982G>A	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"""Poly (ADP-ribose) polymerases"""	272	protein-coding gene	gene with protein product		607725	"""ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2"", ""poly (ADP-ribose) polymerase family, member 2"""	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.817G>A	14.37:g.20822982G>A	ENSP00000250416:p.Ala273Thr					PARP2_ENST00000250416.5_Missense_Mutation_p.A273T|PARP2_ENST00000429687.3_Missense_Mutation_p.A260T	p.A273T			Q9UGN5	PARP2_HUMAN	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)	9	822	+	all_cancers(95;0.00092)	all_lung(585;0.235)	273			PARP alpha-helical.		Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Missense_Mutation	SNP	ENST00000250416.5	37	c.817G>A	CCDS41910.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.706676	0.68615	.	.	ENSG00000129484	ENST00000429687;ENST00000250416;ENST00000527915	T;T;T	0.11604	2.76;2.76;2.76	5.18	4.27	0.50696	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.179769	0.47852	D	0.000215	T	0.08268	0.0206	L	0.33189	0.99	0.47245	D	0.999364	P;P;P	0.42161	0.772;0.562;0.591	B;B;B	0.38194	0.267;0.049;0.158	T	0.33085	-0.9882	10	0.14656	T	0.56	-5.6768	13.1418	0.59438	0.0802:0.0:0.9198:0.0	.	186;260;273	B4DV82;Q9UGN5-2;Q9UGN5	.;.;PARP2_HUMAN	T	260;273;273	ENSP00000392972:A260T;ENSP00000250416:A273T;ENSP00000432283:A273T	ENSP00000250416:A273T	A	+	1	0	PARP2	19892822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.061000	0.64319	2.694000	0.91930	0.655000	0.94253	GCA		0.468	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			4	264	0	0	0	0.217242	0	4	264				
APOBEC3D	140564	broad.mit.edu	37	22	39421246	39421246	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr22:39421246C>T	ENST00000216099.8	+	3	789	c.382C>T	c.(382-384)Ctg>Ttg	p.L128L	APOBEC3D_ENST00000381568.4_Silent_p.L128L|APOBEC3D_ENST00000427494.2_Intron	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	128					defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.L128L(2)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					CAATGTCACCCTGACCATCTC	0.572																																						ENST00000216099.7																			2	Substitution - coding silent(2)	p.L128L(2)	prostate(2)	breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11						c.(382-384)Ctg>Ttg		apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D							85.0	86.0	86.0					22																	39421246		2203	4300	6503	SO:0001819	synonymous_variant	140564				negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding	g.chr22:39421246C>T	BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"""Apolipoprotein B mRNA editing enzymes"""	17354	protein-coding gene	gene with protein product		609900	"""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)"", ""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"""	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.382C>T	22.37:g.39421246C>T						APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_Silent_p.L128L	p.L128L	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN			3	789	+	Melanoma(58;0.04)		128					Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Silent	SNP	ENST00000216099.8	37	c.382C>T	CCDS46709.1																																																																																				0.572	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426		7	103	0	0	0	0.278610	0	7	103				
WASF2	10163	broad.mit.edu	37	1	27755320	27755320	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:27755320G>A	ENST00000430629.2	-	2	296	c.81C>T	c.(79-81)tgC>tgT	p.C27C	WASF2_ENST00000536657.1_Silent_p.C27C	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	27					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)	p.C27C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		TGTTGGTCACGCATTCCAGCT	0.577																																						ENST00000430629.2																			1	Substitution - coding silent(1)	p.C27C(1)	prostate(1)	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18						c.(79-81)tgC>tgT		WAS protein family, member 2							104.0	88.0	93.0					1																	27755320		2203	4296	6499	SO:0001819	synonymous_variant	10163				actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding	g.chr1:27755320G>A	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.81C>T	1.37:g.27755320G>A						WASF2_ENST00000536657.1_Silent_p.C27C	p.C27C	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)	2	296	-		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)	27					B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	37	c.81C>T	CCDS304.1																																																																																				0.577	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		4	140	0	0	0	0.150653	0	4	140				
ZNF518A	9849	broad.mit.edu	37	10	97916435	97916435	+	RNA	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:97916435T>G	ENST00000534948.1	+	0	1213							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F119C(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		ATACTCAATTTCAGCTGTTTA	0.388																																						ENST00000534948.1																			2	Substitution - Missense(2)	p.F119C(2)	prostate(2)	breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24								zinc finger protein 518A							116.0	113.0	114.0					10																	97916435		1853	4093	5946			9849				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr10:97916435T>G	AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"""Zinc fingers, C2H2-type"""	29009	protein-coding gene	gene with protein product			"""zinc finger protein 518"""	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97916435T>G										Q6AHZ1	Z518A_HUMAN		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)	0	1213	+		Colorectal(252;0.0815)						A0PJI5|O15044|Q32MP4	RNA	SNP	ENST00000534948.1	37																																																																																						0.388	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		13	277	0	0	0	0.435327	0	13	277				
TAS2R1	50834	broad.mit.edu	37	5	9629679	9629679	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:9629679G>A	ENST00000382492.2	-	1	784	c.466C>T	c.(466-468)Cta>Tta	p.L156L	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	156					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.L156L(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						AATTTCCTTAGGAAGTATGGG	0.393																																						ENST00000382492.2																			1	Substitution - coding silent(1)	p.L156L(1)	prostate(1)	breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						c.(466-468)Cta>Tta		taste receptor, type 2, member 1							72.0	80.0	77.0					5																	9629679		2203	4300	6503	SO:0001819	synonymous_variant	50834				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity	g.chr5:9629679G>A	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.466C>T	5.37:g.9629679G>A						CTD-2001E22.1_ENST00000504182.2_RNA	p.L156L	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN			1	784	-			156					Q646G8	Silent	SNP	ENST00000382492.2	37	c.466C>T	CCDS3876.1																																																																																				0.393	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			8	151	0	0	0	0.307466	0	8	151				
KMT2D	8085	broad.mit.edu	37	12	49420423	49420423	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:49420423C>A	ENST00000301067.7	-	48	15325	c.15326G>T	c.(15325-15327)tGc>tTc	p.C5109F		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5109			C -> F (in KABUK1). {ECO:0000269|PubMed:20711175}.		chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C5109F(1)|p.C4839F(1)									GACATTGGGGCAACGCATGCG	0.547																																						ENST00000301067.7																			2	Substitution - Missense(2)	p.C5109F(1)|p.C4839F(1)	prostate(2)								c.(15325-15327)tGc>tTc		lysine (K)-specific methyltransferase 2D							67.0	68.0	68.0					12																	49420423		2163	4254	6417	SO:0001583	missense	8085							g.chr12:49420423C>A	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.15326G>T	12.37:g.49420423C>A	ENSP00000301067:p.Cys5109Phe						p.C5109F	NM_003482.3	NP_003473.3					48	15325	-								O14687	Missense_Mutation	SNP	ENST00000301067.7	37	c.15326G>T	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	12.75	2.032824	0.35893	.	.	ENSG00000167548	ENST00000301067	D	0.94330	-3.4	4.77	4.77	0.60923	Zinc finger, RING-type (1);Zinc finger, PHD-type (1);	0.000000	0.39909	N	0.001227	D	0.97826	0.9286	H	0.96269	3.795	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.99271	1.0893	10	0.87932	D	0	.	16.9322	0.86193	0.0:1.0:0.0:0.0	.	5109	O14686	MLL2_HUMAN	F	5109	ENSP00000301067:C5109F	ENSP00000301067:C5109F	C	-	2	0	MLL2	47706690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.377000	0.81083	0.561000	0.74099	TGC		0.547	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			33	71	1	0	2.08457e-15	0.750413	2.5389e-15	33	71				
SCARB1	949	broad.mit.edu	37	12	125348169	125348169	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:125348169G>C	ENST00000415380.2	-	1	223	c.98C>G	c.(97-99)cCg>cGg	p.P33R	SCARB1_ENST00000261693.6_Missense_Mutation_p.P33R|SCARB1_ENST00000376788.1_Missense_Mutation_p.P33R|SCARB1_ENST00000546215.1_Missense_Mutation_p.P33R|SCARB1_ENST00000339570.5_Missense_Mutation_p.P33R|SCARB1_ENST00000535005.1_Intron			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	33					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.P33R(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GATGAGCGACGGCACCATCAC	0.716																																						ENST00000339570.5																			2	Substitution - Missense(2)	p.P33R(2)	prostate(2)	endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17						c.(97-99)cCg>cGg		scavenger receptor class B, member 1	Phosphatidylserine(DB00144)						26.0	23.0	24.0					12																	125348169		2201	4300	6501	SO:0001583	missense	949				adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity	g.chr12:125348169G>C	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"""	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.98C>G	12.37:g.125348169G>C	ENSP00000414979:p.Pro33Arg					SCARB1_ENST00000376788.1_Missense_Mutation_p.P33R|SCARB1_ENST00000535005.1_Intron|SCARB1_ENST00000546215.1_Missense_Mutation_p.P33R|SCARB1_ENST00000415380.2_Missense_Mutation_p.P33R|SCARB1_ENST00000261693.6_Missense_Mutation_p.P33R	p.P33R	NM_001082959.1	NP_001076428.1	Q8WTV0	SCRB1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	1	294	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)		33					F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37	c.98C>G		.	.	.	.	.	.	.	.	.	.	G	15.75	2.924904	0.52759	.	.	ENSG00000073060	ENST00000339570;ENST00000415380;ENST00000261693;ENST00000376788;ENST00000546215;ENST00000545493	T;T;T;D;T;T	0.86297	-0.76;-0.76;-0.76;-2.1;-0.76;-0.76	3.3	3.3	0.37823	.	0.000000	0.85682	U	0.000000	D	0.92100	0.7496	M	0.79614	2.46	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.998;0.995;0.992	D	0.92129	0.5710	10	0.59425	D	0.04	-12.7663	10.7759	0.46350	0.0:0.0:1.0:0.0	.	33;33;33;33;33	B7ZKQ9;B4E3I1;Q8WTV0;F8W8N0;Q8WTV0-2	.;.;SCRB1_HUMAN;.;.	R	33	ENSP00000343795:P33R;ENSP00000414979:P33R;ENSP00000261693:P33R;ENSP00000365984:P33R;ENSP00000442862:P33R;ENSP00000443454:P33R	ENSP00000261693:P33R	P	-	2	0	SCARB1	123914122	0.983000	0.35010	0.998000	0.56505	0.143000	0.21401	3.058000	0.49939	1.778000	0.52293	0.185000	0.17295	CCG		0.716	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		3	15	0	0	0	0.115264	0	3	15				
TBL1XR1	79718	broad.mit.edu	37	3	176755961	176755961	+	Splice_Site	SNP	C	C	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:176755961C>G	ENST00000430069.1	-	12	1307		c.e12-1		TBL1XR1_ENST00000457928.2_Splice_Site			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.?(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTACTTCATTCTAAAAATAAT	0.323																																						ENST00000430069.1																			1	Unknown(1)	p.?(1)	prostate(1)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						c.e12-1		transducin (beta)-like 1 X-linked receptor 1							57.0	55.0	56.0					3																	176755961		1821	4082	5903	SO:0001630	splice_region_variant	79718				canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding	g.chr3:176755961C>G	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.1048-1G>C	3.37:g.176755961C>G						TBL1XR1_ENST00000457928.2_Splice_Site				Q9BZK7	TBL1R_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)		12	1307	-	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)						D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Splice_Site	SNP	ENST00000430069.1	37		CCDS46961.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160938	0.78226	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	.	.	.	5.48	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.778	0.63066	0.0:0.9246:0.0:0.0754	.	.	.	.	.	-1	.	.	.	-	.	.	TBL1XR1	178238655	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.055000	0.71103	2.581000	0.87130	0.585000	0.79938	.		0.323	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665	Intron	4	57	0	0	0	0.184627	0	4	57				
SPTA1	6708	broad.mit.edu	37	1	158612201	158612201	+	Splice_Site	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:158612201C>T	ENST00000368147.4	-	33	4917	c.4737G>A	c.(4735-4737)aaG>aaA	p.K1579K		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1579					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.K1579K(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGAGCTTTACCTTCATGGCCT	0.393																																						ENST00000368148.3																			1	Substitution - coding silent(1)	p.K1579K(1)	prostate(1)	NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307						c.e33+1		spectrin, alpha, erythrocytic 1 (elliptocytosis 2)							117.0	115.0	115.0					1																	158612201		1927	4136	6063	SO:0001630	splice_region_variant	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158612201C>T	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4737+1G>A	1.37:g.158612201C>T						SPTA1_ENST00000368147.3_Splice_Site_p.K1579_splice	p.K1579_splice	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN			33	4917	-	all_hematologic(112;0.0378)		1579					Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Splice_Site	SNP	ENST00000368147.4	37	c.4737_splice	CCDS41423.1																																																																																				0.393	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	Silent	9	269	0	0	0	0.361761	0	9	269				
EHHADH	1962	broad.mit.edu	37	3	184910384	184910384	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:184910384G>A	ENST00000231887.3	-	7	1877	c.1802C>T	c.(1801-1803)tCa>tTa	p.S601L	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Missense_Mutation_p.S505L	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	601					fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)	p.S601L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TCTATACCGTGATAGGAATTT	0.428																																						ENST00000231887.3																			1	Substitution - Missense(1)	p.S601L(1)	prostate(1)	breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24						c.(1801-1803)tCa>tTa		enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	NADH(DB00157)						105.0	97.0	100.0					3																	184910384		2203	4300	6503	SO:0001583	missense	1962					peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity	g.chr3:184910384G>A	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1802C>T	3.37:g.184910384G>A	ENSP00000231887:p.Ser601Leu					EHHADH_ENST00000456310.1_Missense_Mutation_p.S505L	p.S601L	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		7	1877	-	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		601					A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	c.1802C>T	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	G	8.504	0.864954	0.17250	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	T;T	0.75477	-0.53;-0.94	5.91	5.03	0.67393	.	0.594442	0.17849	N	0.159928	T	0.55986	0.1955	N	0.14661	0.345	0.80722	D	1	B	0.30236	0.274	B	0.22386	0.039	T	0.53641	-0.8410	10	0.30078	T	0.28	-3.6632	12.1049	0.53807	0.0658:0.1208:0.8135:0.0	.	601	Q08426	ECHP_HUMAN	L	601;505	ENSP00000231887:S601L;ENSP00000387746:S505L	ENSP00000231887:S601L	S	-	2	0	EHHADH	186393078	0.994000	0.37717	0.087000	0.20705	0.433000	0.31745	3.108000	0.50337	1.503000	0.48686	0.655000	0.94253	TCA		0.428	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			34	227	0	0	0	0.760397	0	34	227				
LAMA2	3908	broad.mit.edu	37	6	129601260	129601260	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:129601260C>T	ENST00000421865.2	+	18	2554	c.2505C>T	c.(2503-2505)tgC>tgT	p.C835C		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	835	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.C835C(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GTGATGGATGCCCTGTCGGGT	0.453																																						ENST00000421865.2																			1	Substitution - coding silent(1)	p.C835C(1)	prostate(1)	NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194						c.(2503-2505)tgC>tgT		laminin, alpha 2							230.0	181.0	197.0					6																	129601260		2203	4300	6503	SO:0001819	synonymous_variant	3908				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity	g.chr6:129601260C>T	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2505C>T	6.37:g.129601260C>T							p.C835C	NM_000426.3|NM_001079823.1	NP_000417.2|NP_001073291.1	P24043	LAMA2_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)	18	2554	+			835			Laminin EGF-like 7.		Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	c.2505C>T	CCDS5138.1																																																																																				0.453	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			4	77	0	0	0	0.150653	0	4	77				
NRG3	10718	broad.mit.edu	37	10	84745233	84745233	+	Missense_Mutation	SNP	G	G	A	rs143042604	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:84745233G>A	ENST00000404547.1	+	10	2035	c.2035G>A	c.(2035-2037)Gta>Ata	p.V679I	NRG3_ENST00000556918.1_Missense_Mutation_p.V485I|NRG3_ENST00000372142.2_Missense_Mutation_p.V458I|NRG3_ENST00000372141.2_Missense_Mutation_p.V655I|NRG3_ENST00000545131.1_Missense_Mutation_p.V305I|NRG3_ENST00000537893.1_Missense_Mutation_p.V305I|NRG3_ENST00000404576.2_Missense_Mutation_p.V459I			P56975	NRG3_HUMAN	neuregulin 3	679					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.V655I(1)|p.V458I(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ACTGGCCAGCGTAGAAACCGA	0.473																																						ENST00000372142.2																			2	Substitution - Missense(2)	p.V655I(1)|p.V458I(1)	prostate(2)	breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(1372-1374)Gta>Ata		neuregulin 3		G	ILE/VAL,ILE/VAL,ILE/VAL	10,4396	16.8+/-37.8	0,10,2193	75.0	70.0	71.0		1963,1960,1372	3.7	1.0	10	dbSNP_134	71	0,8600		0,0,4300	yes	missense,missense,missense	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	29,29,29	0,10,6493	AA,AG,GG		0.0,0.227,0.0769	benign,benign,benign	655/697,654/696,458/500	84745233	10,12996	2203	4300	6503	SO:0001583	missense	10718				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity	g.chr10:84745233G>A	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.2035G>A	10.37:g.84745233G>A	ENSP00000384796:p.Val679Ile					NRG3_ENST00000556918.1_Missense_Mutation_p.V485I|NRG3_ENST00000372141.2_Missense_Mutation_p.V655I|NRG3_ENST00000404547.1_Missense_Mutation_p.V679I|NRG3_ENST00000545131.1_Missense_Mutation_p.V305I|NRG3_ENST00000404576.2_Missense_Mutation_p.V459I|NRG3_ENST00000537893.1_Missense_Mutation_p.V305I	p.V458I	NM_001165973.1	NP_001159445.1	P56975	NRG3_HUMAN		GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)	11	1646	+			679					A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	c.1372G>A	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.867655	0.32977	0.00227	0.0	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.50277	1.38;1.37;1.36;0.75;1.32;0.83;0.83	5.54	3.67	0.42095	.	0.586784	0.17414	N	0.175071	T	0.30916	0.0780	L	0.34521	1.04	0.29478	N	0.856538	B;P;B;P	0.35982	0.004;0.531;0.017;0.531	B;B;B;B	0.28465	0.003;0.09;0.004;0.09	T	0.21008	-1.0258	10	0.49607	T	0.09	-23.7473	7.0275	0.24948	0.2795:0.0:0.7205:0.0	.	654;679;458;655	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	I	655;679;654;458;459;485;305;305	ENSP00000361214:V655I;ENSP00000384796:V679I;ENSP00000361215:V458I;ENSP00000385804:V459I;ENSP00000451376:V485I;ENSP00000441201:V305I;ENSP00000440377:V305I	ENSP00000361214:V655I	V	+	1	0	NRG3	84735213	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.281000	0.33214	0.687000	0.31509	0.655000	0.94253	GTA		0.473	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		45	52	0	0	0	0.840704	0	45	52				
CRISPLD2	83716	broad.mit.edu	37	16	84906612	84906612	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr16:84906612C>T	ENST00000262424.5	+	10	1220	c.996C>T	c.(994-996)tgC>tgT	p.C332C	CRISPLD2_ENST00000564567.1_Silent_p.C332C|CRISPLD2_ENST00000567845.1_Silent_p.C331C	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	332	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)	p.C332C(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						CTAGCATATGCCGCGCCGCCA	0.542																																						ENST00000262424.5																			1	Substitution - coding silent(1)	p.C332C(1)	prostate(1)	endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						c.(994-996)tgC>tgT		cysteine-rich secretory protein LCCL domain containing 2							104.0	101.0	102.0					16																	84906612		2199	4300	6499	SO:0001819	synonymous_variant	83716					extracellular region|transport vesicle		g.chr16:84906612C>T	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.996C>T	16.37:g.84906612C>T						CRISPLD2_ENST00000564567.1_Silent_p.C332C|CRISPLD2_ENST00000567845.1_Silent_p.C331C	p.C332C	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN			10	1220	+			332			LCCL 1.		D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Silent	SNP	ENST00000262424.5	37	c.996C>T	CCDS10949.1																																																																																				0.542	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		5	184	0	0	0	0.184627	0	5	184				
USP38	84640	broad.mit.edu	37	4	144133502	144133502	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr4:144133502A>G	ENST00000307017.4	+	8	2035	c.1529A>G	c.(1528-1530)gAg>gGg	p.E510G	USP38_ENST00000510377.1_Missense_Mutation_p.E510G	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	510	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.E510G(2)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					ATATTCTTTGAGGCTTCCAGA	0.383																																						ENST00000307017.4																			2	Substitution - Missense(2)	p.E510G(2)	prostate(2)	breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33						c.(1528-1530)gAg>gGg		ubiquitin specific peptidase 38							110.0	108.0	108.0					4																	144133502		2203	4300	6503	SO:0001583	missense	84640				ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity	g.chr4:144133502A>G	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1529A>G	4.37:g.144133502A>G	ENSP00000303434:p.Glu510Gly					USP38_ENST00000510377.1_Missense_Mutation_p.E510G	p.E510G	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN			8	2035	+	all_hematologic(180;0.158)		510					B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	37	c.1529A>G	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824903	0.71143	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.33216	1.42;1.42	5.25	4.04	0.47022	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.177179	0.48767	D	0.000161	T	0.30293	0.0760	L	0.41492	1.28	0.54753	D	0.999989	B;P	0.42296	0.387;0.775	B;P	0.45660	0.388;0.489	T	0.01951	-1.1241	10	0.31617	T	0.26	-9.7254	11.6978	0.51553	0.8672:0.0:0.0:0.1328	.	510;510	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	G	510	ENSP00000427647:E510G;ENSP00000303434:E510G	ENSP00000303434:E510G	E	+	2	0	USP38	144352952	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.226000	0.95229	0.919000	0.36945	0.529000	0.55759	GAG		0.383	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		3	232	0	0	0	0.115264	0	3	232				
TPTE2	93492	broad.mit.edu	37	13	20024290	20024290	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr13:20024290A>G	ENST00000400230.2	-	13	943	c.899T>C	c.(898-900)tTc>tCc	p.F300S	TPTE2_ENST00000390680.2_Missense_Mutation_p.F223S|TPTE2_ENST00000457266.2_Missense_Mutation_p.F189S|TPTE2_ENST00000382977.4_Missense_Mutation_p.F300S|TPTE2_ENST00000382978.1_Missense_Mutation_p.F260S|TPTE2_ENST00000400103.2_Missense_Mutation_p.F189S|TPTE2_ENST00000255310.6_Missense_Mutation_p.F223S|TPTE2_ENST00000382975.4_Missense_Mutation_p.F260S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	300	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.F300S(1)|p.F223S(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TTCCTTGGTGAAAACCACCAT	0.323																																						ENST00000400230.2																			2	Substitution - Missense(2)	p.F300S(1)|p.F223S(1)	prostate(2)	NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(898-900)tTc>tCc		transmembrane phosphoinositide 3-phosphatase and tensin homolog 2							42.0	44.0	43.0					13																	20024290		2193	4277	6470	SO:0001583	missense	93492					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr13:20024290A>G	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.899T>C	13.37:g.20024290A>G	ENSP00000383089:p.Phe300Ser					TPTE2_ENST00000390680.2_Missense_Mutation_p.F223S|TPTE2_ENST00000457266.2_Missense_Mutation_p.F189S|TPTE2_ENST00000255310.6_Missense_Mutation_p.F223S|TPTE2_ENST00000382977.4_Missense_Mutation_p.F300S|TPTE2_ENST00000400103.2_Missense_Mutation_p.F189S|TPTE2_ENST00000382975.4_Missense_Mutation_p.F260S|TPTE2_ENST00000382978.1_Missense_Mutation_p.F260S	p.F300S			Q6XPS3	TPTE2_HUMAN		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)	13	943	-		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)	300			Phosphatase tensin-type.		A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	c.899T>C	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	a	11.02	1.515285	0.27123	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.98958	-5.27;-5.27;-5.27;-5.27;-5.27;-5.27;-5.27;-5.27	2.79	1.6	0.23607	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.186835	0.47852	D	0.000201	D	0.98960	0.9646	M	0.91768	3.24	0.09310	N	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.991;0.994;0.991	D	0.95562	0.8630	9	.	.	.	-13.261	6.3107	0.21163	0.8675:0.0:0.1325:0.0	.	189;223;300	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	S	260;189;300;223;223;300;260;189;300;169	ENSP00000372438:F260S;ENSP00000382974:F189S;ENSP00000383089:F300S;ENSP00000255310:F223S;ENSP00000375098:F223S;ENSP00000372437:F300S;ENSP00000372435:F260S;ENSP00000442218:F189S	.	F	-	2	0	TPTE2	18922290	1.000000	0.71417	0.001000	0.08648	0.001000	0.01503	3.464000	0.53057	0.482000	0.27582	-0.480000	0.04831	TTC		0.323	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		11	185	0	0	0	0.500413	0	11	185				
KRTAP3-3	85293	broad.mit.edu	37	17	39150166	39150166	+	Missense_Mutation	SNP	C	C	T	rs146610892	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:39150166C>T	ENST00000391586.1	-	1	219	c.184G>A	c.(184-186)Gtg>Atg	p.V62M		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	62						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.V62M(1)		lung(2)|prostate(2)	4		Breast(137;0.00043)				CAGGTGGGCACGCAGGGCTGA	0.632													C|||	7	0.00139776	0.0053	0.0	5008	,	,		18411	0.0		0.0	False		,,,				2504	0.0					ENST00000391586.1																			1	Substitution - Missense(1)	p.V62M(1)	prostate(1)	lung(2)|prostate(2)	4						c.(184-186)Gtg>Atg		keratin associated protein 3-3		C	MET/VAL	25,4381	31.7+/-61.6	0,25,2178	107.0	78.0	88.0		184	5.9	1.0	17	dbSNP_134	88	2,8586	2.2+/-6.3	0,2,4292	no	missense	KRTAP3-3	NM_033185.2	21	0,27,6470	TT,TC,CC		0.0233,0.5674,0.2078	probably-damaging	62/99	39150166	27,12967	2203	4294	6497	SO:0001583	missense	85293					keratin filament	structural molecule activity	g.chr17:39150166C>T	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"""Keratin associated proteins"""	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.184G>A	17.37:g.39150166C>T	ENSP00000375428:p.Val62Met						p.V62M	NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN			1	219	-		Breast(137;0.00043)	62					Q52LP0|Q6NTD4	Missense_Mutation	SNP	ENST00000391586.1	37	c.184G>A	CCDS32643.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233534	0.79688	0.005674	2.33E-4	ENSG00000212899	ENST00000391586	T	0.32515	1.45	5.89	5.89	0.94794	.	0.000000	0.51477	D	0.000090	T	0.49864	0.1582	.	.	.	0.39246	D	0.963944	D	0.89917	1.0	D	0.91635	0.999	T	0.60156	-0.7318	9	0.87932	D	0	.	15.8129	0.78578	0.0:1.0:0.0:0.0	.	62	Q9BYR6	KRA33_HUMAN	M	62	ENSP00000375428:V62M	ENSP00000375428:V62M	V	-	1	0	KRTAP3-3	36403692	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.511000	0.53400	2.801000	0.96364	0.650000	0.86243	GTG		0.632	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1			5	149	0	0	0	0.184627	0	5	149				
LINC00518	221718	broad.mit.edu	37	6	10430364	10430364	+	lincRNA	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:10430364T>C	ENST00000496285.1	-	0	671					NR_027793.1		Q8N0U6	CF218_HUMAN	long intergenic non-protein coding RNA 518									p.S42G(1)									atttggtcactctCATTGAGG	0.443																																						ENST00000496285.1																			1	Substitution - Missense(1)	p.S42G(1)	prostate(1)																	120.0	125.0	123.0					6																	10430364		2203	4300	6503			0							g.chr6:10430364T>C	BC028118		6p24.3	2014-06-18	2011-11-25	2011-11-25	ENSG00000183674	ENSG00000183674		"""Long non-coding RNAs"""	28626	non-coding RNA	RNA, long non-coding			"""chromosome 6 open reading frame 218"""	C6orf218		12477932, 24906614	Standard	NR_027793		Approved	MGC40222	uc003myz.2	Q8N0U6	OTTHUMG00000159175		6.37:g.10430364T>C								NR_027793.1						0	671	-									RNA	SNP	ENST00000496285.1	37																																																																																						0.443	LINC00518-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000353699.1	NR_027793		3	178	0	0	0	0.115264	0	3	178				
ARID4B	51742	broad.mit.edu	37	1	235345029	235345029	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:235345029T>C	ENST00000264183.3	-	20	3702	c.3205A>G	c.(3205-3207)Att>Gtt	p.I1069V	ARID4B_ENST00000349213.3_Missense_Mutation_p.I983V|ARID4B_ENST00000366603.2_Missense_Mutation_p.I1069V|ARID4B_ENST00000494543.1_5'UTR	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1069					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I1069V(1)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCCACCTCAATTGTGCTATCA	0.493																																						ENST00000264183.3																			1	Substitution - Missense(1)	p.I1069V(1)	prostate(1)	NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8						c.(3205-3207)Att>Gtt		AT rich interactive domain 4B (RBP1-like)							112.0	92.0	99.0					1																	235345029		2203	4300	6503	SO:0001583	missense	51742				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding	g.chr1:235345029T>C	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.3205A>G	1.37:g.235345029T>C	ENSP00000264183:p.Ile1069Val					ARID4B_ENST00000349213.3_Missense_Mutation_p.I983V|ARID4B_ENST00000494543.1_5'UTR|ARID4B_ENST00000366603.2_Missense_Mutation_p.I1069V	p.I1069V	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)		20	3702	-	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	1069					A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	c.3205A>G	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.523373	0.44866	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183	T;T;T	0.22945	1.93;1.96;1.96	5.17	5.17	0.71159	.	0.063541	0.64402	D	0.000005	T	0.42223	0.1193	L	0.42686	1.345	0.54753	D	0.999986	P;P;P;P	0.51791	0.948;0.826;0.899;0.734	D;P;P;P	0.67103	0.949;0.811;0.683;0.651	T	0.16928	-1.0386	10	0.44086	T	0.13	-13.3003	15.0333	0.71725	0.0:0.0:0.0:1.0	.	750;1069;983;1069	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	V	1069;983;1069;1069	ENSP00000264184:I983V;ENSP00000355562:I1069V;ENSP00000264183:I1069V	ENSP00000264183:I1069V	I	-	1	0	ARID4B	233411652	0.993000	0.37304	0.998000	0.56505	0.992000	0.81027	2.389000	0.44407	1.959000	0.56917	0.477000	0.44152	ATT		0.493	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		32	54	0	0	0	0.729181	0	32	54				
CCT6P1	643253	broad.mit.edu	37	7	65222986	65222986	+	RNA	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:65222986G>T	ENST00000442266.1	+	0	578				SNORA15_ENST00000384058.1_RNA|SNORA22_ENST00000383907.1_RNA					chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1																		GAATTCTGGCGTTTTTTACAA	0.289																																						ENST00000442266.1																			0																																																			0							g.chr7:65222986G>T	BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409			33094	pseudogene	pseudogene			"""chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1"""	CCT6AP1			Standard	NR_003110		Approved		uc003tug.3		OTTHUMG00000156733		7.37:g.65222986G>T														0	578	+									RNA	SNP	ENST00000442266.1	37																																																																																						0.289	CCT6P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345507.1	NR_003110		4	28	1	0	5.9392e-07	0.217242	7.14208e-07	4	28				
MSH3	4437	broad.mit.edu	37	5	79961132	79961132	+	Missense_Mutation	SNP	G	G	A	rs372073889		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:79961132G>A	ENST00000265081.6	+	3	609	c.529G>A	c.(529-531)Gca>Aca	p.A177T		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	177	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)	p.A168T(1)|p.A177T(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCTTCTACACGCAAAGAATGC	0.388								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			2	Substitution - Missense(2)	p.A168T(1)|p.A177T(1)	prostate(2)	NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(529-531)Gca>Aca	Mismatch excision repair (MMR)	mutS homolog 3		G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	59.0	57.0	58.0		529	4.7	1.0	5		58	0,8600		0,0,4300	no	missense	MSH3	NM_002439.3	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	177/1138	79961132	1,13005	2203	4300	6503	SO:0001583	missense	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79961132G>A	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.529G>A	5.37:g.79961132G>A	ENSP00000265081:p.Ala177Thr						p.A177T	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	3	609	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	177			Interaction with EXO1.		A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	c.529G>A	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.658939	0.29515	2.27E-4	0.0	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.87179	-2.22	5.62	4.69	0.59074	.	0.475283	0.21461	N	0.074168	T	0.81202	0.4773	L	0.52573	1.65	0.31133	N	0.707508	B	0.29037	0.231	B	0.17722	0.019	T	0.77832	-0.2441	9	.	.	.	-20.0476	10.9953	0.47571	0.0:0.0:0.8142:0.1858	.	177	P20585	MSH3_HUMAN	T	177;168	ENSP00000265081:A177T	.	A	+	1	0	MSH3	79996888	0.996000	0.38824	0.991000	0.47740	0.365000	0.29674	2.085000	0.41634	2.640000	0.89533	0.591000	0.81541	GCA		0.388	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		45	67	0	0	0	0.870114	0	45	67				
GSTM5	2949	broad.mit.edu	37	1	110256100	110256100	+	Intron	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:110256100A>G	ENST00000256593.3	+	4	235				GSTM5_ENST00000369812.5_Missense_Mutation_p.I77V|GSTM5_ENST00000369813.1_Missense_Mutation_p.I17V	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5						glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)	p.?(1)		NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	TTTCCCATCTATCCAGCTGCC	0.592																																						ENST00000369813.1																			1	Unknown(1)	p.?(1)	prostate(1)	NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21						c.(49-51)Atc>Gtc		glutathione S-transferase mu 5	Glutathione(DB00143)						196.0	162.0	174.0					1																	110256100		2203	4297	6500	SO:0001627	intron_variant	2949				xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity	g.chr1:110256100A>G	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.178-6A>G	1.37:g.110256100A>G						GSTM5_ENST00000256593.3_Intron|GSTM5_ENST00000369812.5_Missense_Mutation_p.I77V	p.I17V			P46439	GSTM5_HUMAN		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	2	954	+		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)	59			GST N-terminal.		A8K0V8|Q6PD78	Missense_Mutation	SNP	ENST00000256593.3	37	c.49A>G	CCDS811.1	.	.	.	.	.	.	.	.	.	.	A	1.012	-0.687450	0.03328	.	.	ENSG00000134201	ENST00000369813;ENST00000369812	T;T	0.06218	3.33;3.33	0.149	-0.298	0.12814	.	.	.	.	.	T	0.01661	0.0053	.	.	.	0.09310	N	1	P	0.35944	0.529	B	0.38562	0.276	T	0.43196	-0.9406	7	0.59425	D	0.04	.	.	.	.	.	17	Q5T8Q9	.	V	17;77	ENSP00000358828:I17V;ENSP00000358827:I77V	ENSP00000358827:I77V	I	+	1	0	GSTM5	110057623	.	.	0.002000	0.10522	0.025000	0.11179	.	.	-1.231000	0.02557	-1.266000	0.01441	ATC		0.592	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851		84	186	0	0	0	0.870114	0	84	186				
KMT2C	58508	broad.mit.edu	37	7	151845758	151845758	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151845758C>A	ENST00000262189.6	-	52	13472	c.13254G>T	c.(13252-13254)agG>agT	p.R4418S	KMT2C_ENST00000355193.2_Missense_Mutation_p.R4475S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4418					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)	p.R4418S(1)|p.R4475S(1)									GGTTGAGTAGCCTTGCTGGTC	0.488																																						ENST00000355193.2																			2	Substitution - Missense(2)	p.R4418S(1)|p.R4475S(1)	prostate(2)								c.(13423-13425)agG>agT		lysine (K)-specific methyltransferase 2C							93.0	85.0	87.0					7																	151845758		2203	4300	6503	SO:0001583	missense	58508							g.chr7:151845758C>A	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.13254G>T	7.37:g.151845758C>A	ENSP00000262189:p.Arg4418Ser					KMT2C_ENST00000262189.6_Missense_Mutation_p.R4418S	p.R4475S							53	13643	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	c.13425G>T	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.90|14.90	2.673089|2.673089	0.47781|0.47781	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193;ENST00000424877	.|D;D;D	.|0.90844	.|-2.15;-2.13;-2.74	5.24|5.24	4.33|4.33	0.51752|0.51752	.|.	.|0.000000	.|0.47455	.|U	.|0.000223	D|D	0.94430|0.94430	0.8208|0.8208	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.997;1.0;1.0	.|D;D;D	.|0.85130	.|0.977;0.997;0.997	D|D	0.94395|0.94395	0.7617|0.7617	5|10	.|0.87932	.|D	.|0	.|.	10.6467|10.6467	0.45623|0.45623	0.0:0.8391:0.0:0.1609|0.0:0.8391:0.0:0.1609	.|.	.|4418;3536;4475	.|Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	.|MLL3_HUMAN;.;.	S|S	1979|4418;4475;1035	.|ENSP00000262189:R4418S;ENSP00000347325:R4475S;ENSP00000410411:R1035S	.|ENSP00000262189:R4418S	A|R	-|-	1|3	0|2	MLL3|MLL3	151476691|151476691	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.974000|0.974000	0.67602|0.67602	1.621000|1.621000	0.36986|0.36986	1.271000|1.271000	0.44313|0.44313	0.557000|0.557000	0.71058|0.71058	GCT|AGG		0.488	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			5	172	1	0	0.000602214	0.184627	0.000706301	5	172				
DET1	55070	broad.mit.edu	37	15	89074916	89074916	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:89074916G>A	ENST00000268148.8	-	2	166	c.21C>T	c.(19-21)acC>acT	p.T7T	DET1_ENST00000564406.1_Silent_p.T18T|DET1_ENST00000559656.1_5'Flank|DET1_ENST00000444300.1_Silent_p.T18T|DET1_ENST00000558413.1_Silent_p.T7T	NM_001144074.1	NP_001137546.1	Q7L5Y6	DET1_HUMAN	de-etiolated homolog 1 (Arabidopsis)	7						nucleus (GO:0005634)		p.T18T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			GAGGCTTGATGGTAGAAACAT	0.413																																						ENST00000564406.1																			1	Substitution - coding silent(1)	p.T18T(1)	prostate(1)	endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(52-54)acC>acT		de-etiolated homolog 1 (Arabidopsis)							77.0	75.0	75.0					15																	89074916		1927	4148	6075	SO:0001819	synonymous_variant	55070					nucleus		g.chr15:89074916G>A	BC001242	CCDS45343.1, CCDS45344.1	15q25.3	2004-12-13				ENSG00000140543			25477	protein-coding gene	gene with protein product		608727				14739464	Standard	NM_001144074		Approved	FLJ10103	uc002bmq.2	Q7L5Y6		ENST00000268148.8:c.21C>T	15.37:g.89074916G>A						DET1_ENST00000558413.1_Silent_p.T7T|DET1_ENST00000444300.1_Silent_p.T18T|DET1_ENST00000268148.8_Silent_p.T7T	p.T18T	NM_017996.3	NP_060466.2	Q7L5Y6	DET1_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.188)		3	214	-	Lung NSC(78;0.105)|all_lung(78;0.182)		7					B3KNN6|Q2VPC0|Q9NWD5	Silent	SNP	ENST00000268148.8	37	c.54C>T	CCDS45344.1																																																																																				0.413	DET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415442.2	NM_017996		3	106	0	0	0	0.115264	0	3	106				
MED16	10025	broad.mit.edu	37	19	881676	881676	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:881676G>T	ENST00000589119.1	-	6	1023	c.1024C>A	c.(1024-1026)Cta>Ata	p.L342I	MED16_ENST00000395808.3_Missense_Mutation_p.L342I|MED16_ENST00000325464.1_Missense_Mutation_p.L342I|MED16_ENST00000312090.6_Missense_Mutation_p.L342I|MED16_ENST00000269814.4_Missense_Mutation_p.L342I|MED16_ENST00000606828.1_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	342					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.L342I(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGGCCGATAGGATCCGCCAT	0.577																																						ENST00000312090.6																			1	Substitution - Missense(1)	p.L342I(1)	prostate(1)	NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21						c.(1024-1026)Cta>Ata		mediator complex subunit 16							105.0	95.0	98.0					19																	881676		2203	4295	6498	SO:0001583	missense	10025				androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding	g.chr19:881676G>T	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1024C>A	19.37:g.881676G>T	ENSP00000464810:p.Leu342Ile					MED16_ENST00000325464.1_Missense_Mutation_p.L342I|MED16_ENST00000395808.3_Missense_Mutation_p.L342I|MED16_ENST00000606828.1_Intron|MED16_ENST00000269814.4_Missense_Mutation_p.L342I|MED16_ENST00000589119.1_Missense_Mutation_p.L342I	p.L342I			Q9Y2X0	MED16_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	7	1174	-		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)	342					Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	c.1024C>A	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668353	0.88348	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000424039	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	4.46	4.46	0.54185	WD40 repeat-like-containing domain (2);	0.000000	0.64402	D	0.000001	T	0.64461	0.2600	L	0.56769	1.78	0.80722	D	1	D;D;D;D;D	0.76494	0.996;0.997;0.998;0.998;0.999	D;D;D;D;D	0.83275	0.986;0.987;0.996;0.99;0.994	T	0.64183	-0.6467	10	0.38643	T	0.18	15.9044	16.1288	0.81412	0.0:0.0:1.0:0.0	.	342;342;342;342;342	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	I	342;342;342;342;342;198;342	ENSP00000325612:L342I;ENSP00000308528:L342I;ENSP00000379153:L342I;ENSP00000269814:L342I	ENSP00000269814:L342I	L	-	1	2	MED16	832676	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.136000	0.94489	2.036000	0.60181	0.561000	0.74099	CTA		0.577	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		4	136	1	0	0.184627	0.184627	0.194884	4	136				
PCNXL4	64430	broad.mit.edu	37	14	60591549	60591549	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:60591549A>G	ENST00000406854.1	+	9	3214	c.2660A>G	c.(2659-2661)gAc>gGc	p.D887G	PCNXL4_ENST00000406949.1_Missense_Mutation_p.D653G|PCNXL4_ENST00000535349.1_Missense_Mutation_p.D94G|PCNXL4_ENST00000317623.4_Missense_Mutation_p.D653G|PCNXL4_ENST00000404681.2_Missense_Mutation_p.D887G			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	887						integral component of membrane (GO:0016021)		p.D653G(1)|p.D887G(1)									CCTGCTGTTGACAAAGGAAAA	0.438																																						ENST00000406854.1																			2	Substitution - Missense(2)	p.D653G(1)|p.D887G(1)	prostate(2)								c.(2659-2661)gAc>gGc		pecanex-like 4 (Drosophila)							123.0	130.0	128.0					14																	60591549		2203	4300	6503	SO:0001583	missense	64430							g.chr14:60591549A>G	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.2660A>G	14.37:g.60591549A>G	ENSP00000384801:p.Asp887Gly					PCNXL4_ENST00000404681.2_Missense_Mutation_p.D887G|PCNXL4_ENST00000317623.4_Missense_Mutation_p.D653G|PCNXL4_ENST00000535349.1_Missense_Mutation_p.D94G|PCNXL4_ENST00000406949.1_Missense_Mutation_p.D653G	p.D887G							9	3214	+								A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37	c.2660A>G		.	.	.	.	.	.	.	.	.	.	A	13.98	2.397405	0.42512	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.40756	1.43;1.46;1.39;1.46;1.02	4.99	3.84	0.44239	.	0.131302	0.64402	D	0.000002	T	0.40979	0.1139	M	0.65975	2.015	0.80722	D	1	B;B	0.26577	0.153;0.125	B;B	0.27076	0.076;0.028	T	0.45041	-0.9288	10	0.56958	D	0.05	.	10.3322	0.43829	0.9219:0.0:0.0781:0.0	.	887;653	Q63HM2;B5MC47	CN135_HUMAN;.	G	653;887;653;887;94	ENSP00000317396:D653G;ENSP00000384801:D887G;ENSP00000385201:D653G;ENSP00000385713:D887G;ENSP00000445644:D94G	ENSP00000317396:D653G	D	+	2	0	C14orf135	59661302	1.000000	0.71417	0.997000	0.53966	0.720000	0.41350	6.681000	0.74523	1.999000	0.58509	0.254000	0.18369	GAC		0.438	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		13	384	0	0	0	0.435327	0	13	384				
TRAM2	9697	broad.mit.edu	37	6	52400646	52400646	+	Splice_Site	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:52400646T>A	ENST00000182527.3	-	2	120		c.e2-2			NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN	translocation associated membrane protein 2						collagen biosynthetic process (GO:0032964)|protein transport (GO:0015031)	integral component of membrane (GO:0016021)		p.?(1)		endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13	Lung NSC(77;0.109)					GGCTGTGACCTGTAAAACAAA	0.438																																						ENST00000182527.3																			1	Unknown(1)	p.?(1)	prostate(1)	endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13						c.e2-2		translocation associated membrane protein 2							84.0	82.0	83.0					6																	52400646		2203	4300	6503	SO:0001630	splice_region_variant	9697				collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding	g.chr6:52400646T>A	D31762	CCDS34477.1	6p21.1-p12	2008-02-05			ENSG00000065308	ENSG00000065308			16855	protein-coding gene	gene with protein product		608485				7584044, 10594243	Standard	NM_012288		Approved	KIAA0057	uc003paq.3	Q15035	OTTHUMG00000014850	ENST00000182527.3:c.121-2A>T	6.37:g.52400646T>A								NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN			2	120	-	Lung NSC(77;0.109)							A8K6T6	Splice_Site	SNP	ENST00000182527.3	37		CCDS34477.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.007403	0.75046	.	.	ENSG00000065308	ENST00000182527	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7881	0.57518	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRAM2	52508605	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.485000	0.60279	2.071000	0.62044	0.533000	0.62120	.		0.438	TRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040910.1	NM_012288	Intron	3	88	0	0	0	0.115264	0	3	88				
ZKSCAN7	55888	broad.mit.edu	37	3	44612332	44612332	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:44612332A>G	ENST00000273320.3	+	6	2159	c.1730A>G	c.(1729-1731)aAg>aGg	p.K577R	RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000341840.3_Intron|RP11-944L7.5_ENST00000419137.1_Intron|ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.K577R	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	577					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K577R(1)									ACTGGGGAAAAGCCATACAAA	0.433																																						ENST00000273320.3																			1	Substitution - Missense(1)	p.K577R(1)	prostate(1)								c.(1729-1731)aAg>aGg		zinc finger with KRAB and SCAN domains 7							92.0	93.0	93.0					3																	44612332		2203	4300	6503	SO:0001583	missense	55888							g.chr3:44612332A>G	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12955	protein-coding gene	gene with protein product			"""zinc finger protein 64"", ""zinc finger protein 448"", ""zinc finger protein 167"""	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.1730A>G	3.37:g.44612332A>G	ENSP00000273320:p.Lys577Arg					ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.K577R|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000431636.1_Intron	p.K577R	NM_018651.2	NP_061121.2					6	2159	+								A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Missense_Mutation	SNP	ENST00000273320.3	37	c.1730A>G	CCDS2715.1	.	.	.	.	.	.	.	.	.	.	.	15.63	2.890354	0.52014	.	.	ENSG00000196345	ENST00000426540;ENST00000273320;ENST00000315777	T;T	0.24908	1.83;1.83	4.21	3.06	0.35304	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.294261	0.18847	N	0.129502	T	0.15392	0.0371	N	0.16790	0.44	0.80722	D	1	B	0.18461	0.028	B	0.19148	0.024	T	0.05099	-1.0906	10	0.56958	D	0.05	-11.2975	8.4961	0.33130	0.9056:0.0:0.0944:0.0	.	577	Q9P0L1	ZN167_HUMAN	R	577;577;15	ENSP00000395524:K577R;ENSP00000273320:K577R	ENSP00000273320:K577R	K	+	2	0	ZNF167	44587336	0.264000	0.24093	0.976000	0.42696	0.811000	0.45836	1.130000	0.31393	0.688000	0.31529	0.533000	0.62120	AAG		0.433	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		3	254	0	0	0	0.115264	0	3	254				
GALNT11	63917	broad.mit.edu	37	7	151814291	151814291	+	Missense_Mutation	SNP	A	A	G	rs202052372		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151814291A>G	ENST00000434507.1	+	11	1720	c.1283A>G	c.(1282-1284)aAt>aGt	p.N428S	GALNT11_ENST00000430044.2_Missense_Mutation_p.N428S|GALNT11_ENST00000452146.2_Missense_Mutation_p.N347S|RP5-981O7.2_ENST00000424630.1_RNA|GALNT11_ENST00000320311.2_Missense_Mutation_p.N428S			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	428					cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.N428S(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGCTATGGCAATATCAGTGAG	0.348																																						ENST00000434507.1																			1	Substitution - Missense(1)	p.N428S(1)	prostate(1)	breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27						c.(1282-1284)aAt>aGt		UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)							142.0	143.0	143.0					7																	151814291		2203	4300	6503	SO:0001583	missense	63917					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr7:151814291A>G	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19875	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 11"""	615130	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"""			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.1283A>G	7.37:g.151814291A>G	ENSP00000416787:p.Asn428Ser					GALNT11_ENST00000320311.2_Missense_Mutation_p.N428S|GALNT11_ENST00000430044.2_Missense_Mutation_p.N428S|GALNT11_ENST00000452146.2_Missense_Mutation_p.N347S	p.N428S			Q8NCW6	GLT11_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)	11	1720	+	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	428					B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Missense_Mutation	SNP	ENST00000434507.1	37	c.1283A>G	CCDS5930.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172794	0.78452	.	.	ENSG00000178234	ENST00000430044;ENST00000452146;ENST00000443352;ENST00000434507;ENST00000320311	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.71	5.71	0.89125	.	0.050407	0.85682	D	0.000000	T	0.33235	0.0856	L	0.38175	1.15	0.80722	D	1	P;D;P	0.54772	0.864;0.968;0.864	B;P;B	0.47744	0.354;0.556;0.407	T	0.10042	-1.0647	10	0.87932	D	0	.	14.5627	0.68151	1.0:0.0:0.0:0.0	.	347;428;428	B7Z5G5;B3KWF4;Q8NCW6	.;.;GLT11_HUMAN	S	428;347;428;428;428	ENSP00000395122:N428S;ENSP00000393399:N347S;ENSP00000416787:N428S;ENSP00000315835:N428S	ENSP00000315835:N428S	N	+	2	0	GALNT11	151445224	1.000000	0.71417	0.278000	0.24718	0.952000	0.60782	9.065000	0.93941	2.168000	0.68352	0.459000	0.35465	AAT		0.348	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		104	238	0	0	0	0.870114	0	104	238				
CRMP1	1400	broad.mit.edu	37	4	5837779	5837779	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr4:5837779C>T	ENST00000397890.2	-	11	1358	c.1144G>A	c.(1144-1146)Gct>Act	p.A382T	CRMP1_ENST00000324989.7_Missense_Mutation_p.A496T|CRMP1_ENST00000512574.1_Missense_Mutation_p.A380T|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	382					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.A496T(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CTGGTGACAGCGACAAACTGG	0.567																																						ENST00000324989.7																			1	Substitution - Missense(1)	p.A496T(1)	prostate(1)	NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36						c.(1486-1488)Gct>Act		collapsin response mediator protein 1							122.0	110.0	114.0					4																	5837779		2203	4300	6503	SO:0001583	missense	1400				axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding	g.chr4:5837779C>T	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1144G>A	4.37:g.5837779C>T	ENSP00000380987:p.Ala382Thr					CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Missense_Mutation_p.A380T|CRMP1_ENST00000397890.2_Missense_Mutation_p.A382T	p.A496T	NM_001014809.1	NP_001014809.1	Q14194	DPYL1_HUMAN		Colorectal(103;0.0721)	11	1574	-			382					A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	c.1486G>A	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572075	0.86542	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.90261	-2.64;-2.64;-2.64	4.22	3.38	0.38709	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.94032	0.8088	M	0.86420	2.815	0.80722	D	1	D;D;D;P	0.67145	0.986;0.996;0.985;0.939	P;P;P;P	0.57101	0.769;0.813;0.769;0.596	D	0.94293	0.7530	10	0.87932	D	0	-10.5965	11.5451	0.50688	0.0:0.9117:0.0:0.0883	.	496;380;382;319	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	T	496;382;382;380	ENSP00000321606:A496T;ENSP00000380987:A382T;ENSP00000425742:A380T	ENSP00000321606:A496T	A	-	1	0	CRMP1	5888680	1.000000	0.71417	0.265000	0.24526	0.935000	0.57460	5.607000	0.67648	1.131000	0.42111	0.508000	0.49915	GCT		0.567	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		77	143	0	0	0	0.870114	0	77	143				
CCDC85A	114800	broad.mit.edu	37	2	56603059	56603059	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:56603059C>A	ENST00000407595.2	+	5	2063	c.1561C>A	c.(1561-1563)Cat>Aat	p.H521N	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	521								p.H521N(1)		breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACCTGTGGTACATTCTCTTAA	0.498																																						ENST00000407595.2																			1	Substitution - Missense(1)	p.H521N(1)	prostate(1)	breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38						c.(1561-1563)Cat>Aat		coiled-coil domain containing 85A							76.0	76.0	76.0					2																	56603059		2045	4194	6239	SO:0001583	missense	114800							g.chr2:56603059C>A	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.1561C>A	2.37:g.56603059C>A	ENSP00000384040:p.His521Asn					RP11-482H16.1_ENST00000607540.1_RNA	p.H521N	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)		5	2063	+			521						Missense_Mutation	SNP	ENST00000407595.2	37	c.1561C>A	CCDS46290.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094606	0.36952	.	.	ENSG00000055813	ENST00000407595;ENST00000407862	.	.	.	5.57	5.57	0.84162	.	0.311378	0.23910	N	0.043346	T	0.40767	0.1130	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25398	-1.0133	9	0.45353	T	0.12	-28.5804	12.3807	0.55305	0.2119:0.7881:0.0:0.0	.	521	Q96PX6	CC85A_HUMAN	N	521;110	.	ENSP00000384040:H521N	H	+	1	0	CCDC85A	56456563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.396000	0.52565	2.615000	0.88500	0.467000	0.42956	CAT		0.498	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1			32	60	1	0	1.836e-18	0.788014	2.3256e-18	32	60				
PHF20	51230	broad.mit.edu	37	20	34389529	34389529	+	Splice_Site	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:34389529T>G	ENST00000374012.3	+	2	212		c.e2+2		PHF20_ENST00000439301.1_Splice_Site|PHF20_ENST00000481202.1_Splice_Site			Q9BVI0	PHF20_HUMAN	PHD finger protein 20						chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.?(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AAAAAACTGGTACTTTTACAT	0.413																																						ENST00000374012.3																			1	Unknown(1)	p.?(1)	prostate(1)	breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.e2+2		PHD finger protein 20							48.0	45.0	46.0					20																	34389529		2203	4300	6503	SO:0001630	splice_region_variant	51230				regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding	g.chr20:34389529T>G	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.83+2T>G	20.37:g.34389529T>G						PHF20_ENST00000439301.1_Splice_Site|PHF20_ENST00000481202.1_Splice_Site				Q9BVI0	PHF20_HUMAN			2	212	+	Breast(12;0.00631)|all_lung(11;0.0145)							A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Splice_Site	SNP	ENST00000374012.3	37		CCDS13268.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228503	0.79576	.	.	ENSG00000025293	ENST00000374012;ENST00000439301;ENST00000339089;ENST00000374000	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4687	0.67501	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PHF20	33852943	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.026000	0.64103	2.049000	0.60858	0.459000	0.35465	.		0.413	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	Intron	4	74	0	0	0	0.150653	0	4	74				
CUBN	8029	broad.mit.edu	37	10	17032435	17032435	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:17032435C>T	ENST00000377833.4	-	29	4313	c.4248G>A	c.(4246-4248)gaG>gaA	p.E1416E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1416	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.E1416E(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACCAGATACACTCCTTGTTTG	0.517																																						ENST00000377833.4																			1	Substitution - coding silent(1)	p.E1416E(1)	prostate(1)	breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241						c.(4246-4248)gaG>gaA		cubilin (intrinsic factor-cobalamin receptor)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)						147.0	139.0	142.0					10																	17032435		2203	4300	6503	SO:0001819	synonymous_variant	8029				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity	g.chr10:17032435C>T	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.4248G>A	10.37:g.17032435C>T							p.E1416E	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN			29	4313	-			1416			CUB 9.		B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	c.4248G>A	CCDS7113.1																																																																																				0.517	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		13	147	0	0	0	0.435327	0	13	147				
TLK1	9874	broad.mit.edu	37	2	171862701	171862701	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:171862701A>G	ENST00000431350.2	-	18	2264	c.1860T>C	c.(1858-1860)ggT>ggC	p.G620G	TLK1_ENST00000434911.2_Silent_p.G524G|TLK1_ENST00000360843.3_Silent_p.G641G|TLK1_ENST00000442919.2_Silent_p.G572G|TLK1_ENST00000521943.1_Silent_p.G572G			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	620	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G572G(2)|p.G620G(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTCCATCTACACCATAGCTAT	0.398																																						ENST00000442919.2																			3	Substitution - coding silent(3)	p.G572G(2)|p.G620G(1)	prostate(3)	breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						c.(1714-1716)ggT>ggC		tousled-like kinase 1							129.0	122.0	124.0					2																	171862701		2203	4300	6503	SO:0001819	synonymous_variant	9874				cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr2:171862701A>G	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1860T>C	2.37:g.171862701A>G						TLK1_ENST00000360843.3_Silent_p.G641G|TLK1_ENST00000431350.2_Silent_p.G620G|TLK1_ENST00000521943.1_Silent_p.G572G|TLK1_ENST00000434911.2_Silent_p.G524G	p.G572G	NM_012290.4	NP_036422.3	Q9UKI8	TLK1_HUMAN			18	2331	-			620			Protein kinase.		B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Silent	SNP	ENST00000431350.2	37	c.1716T>C	CCDS2241.1																																																																																				0.398	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290		15	213	0	0	0	0.520397	0	15	213				
USP19	10869	broad.mit.edu	37	3	49147711	49147711	+	Missense_Mutation	SNP	C	C	A	rs370275115		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:49147711C>A	ENST00000398888.2	-	25	3953	c.3635G>T	c.(3634-3636)cGc>cTc	p.R1212L	USP19_ENST00000453664.1_Missense_Mutation_p.R1303L|USP19_ENST00000434032.2_Missense_Mutation_p.R1313L|USP19_ENST00000398898.2_Missense_Mutation_p.R1252L|USP19_ENST00000398896.1_Missense_Mutation_p.R1020L|USP19_ENST00000417901.1_Missense_Mutation_p.R1315L|USP19_ENST00000398892.3_Missense_Mutation_p.R1252L	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1212	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)	p.R1300L(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTCCGCCGGCGGTAGAAGAG	0.617																																						ENST00000453664.1																			1	Substitution - Missense(1)	p.R1300L(1)	prostate(1)	NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						c.(3907-3909)cGc>cTc		ubiquitin specific peptidase 19							50.0	55.0	53.0					3																	49147711		1994	4165	6159	SO:0001583	missense	10869				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	g.chr3:49147711C>A	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.3635G>T	3.37:g.49147711C>A	ENSP00000381863:p.Arg1212Leu					USP19_ENST00000417901.1_Missense_Mutation_p.R1315L|USP19_ENST00000398898.2_Missense_Mutation_p.R1252L|USP19_ENST00000434032.2_Missense_Mutation_p.R1313L|USP19_ENST00000398888.2_Missense_Mutation_p.R1212L|USP19_ENST00000398892.3_Missense_Mutation_p.R1252L|USP19_ENST00000398896.1_Missense_Mutation_p.R1020L	p.R1303L	NM_001199161.1|NM_001199162.1	NP_001186090.1|NP_001186091.1	O94966	UBP19_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	26	4226	-			1212					A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	c.3908G>T	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897958	0.91962	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.67	5.67	0.87782	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (1);	0.836580	0.11019	N	0.608550	T	0.60663	0.2286	M	0.72479	2.2	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.999	D;D;D;D;D	0.87578	0.998;0.994;0.997;0.987;0.989	T	0.58148	-0.7687	10	0.87932	D	0	-16.1263	19.7629	0.96329	0.0:1.0:0.0:0.0	.	1313;1303;1212;1252;1020	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	L	1020;1252;1315;1303;1252;1212;1313	ENSP00000381870:R1020L;ENSP00000381872:R1252L;ENSP00000395260:R1315L;ENSP00000400090:R1303L;ENSP00000381867:R1252L;ENSP00000381863:R1212L;ENSP00000401197:R1313L	ENSP00000381863:R1212L	R	-	2	0	USP19	49122715	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.476000	0.81055	2.666000	0.90696	0.561000	0.74099	CGC		0.617	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		3	103	1	0	0.115264	0.115264	0.123035	3	103				
LOC220729	220729	broad.mit.edu	37	3	197348668	197348668	+	RNA	SNP	C	C	G	rs79940815	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:197348668C>G	ENST00000418868.1	-	0	591					NR_003266.2																						ACTTGAGGCTCTGTCCACCAA	0.488													C|||	539	0.107628	0.0083	0.0692	5008	,	,		20710	0.1776		0.1074	False		,,,				2504	0.1973					ENST00000418868.1																			0																																																			0							g.chr3:197348668C>G																													3.37:g.197348668C>G								NR_003266.2						0	591	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.488	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			4	194	0	0	0	0.150653	0	4	194				
USP12	219333	broad.mit.edu	37	13	27649444	27649444	+	Silent	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr13:27649444T>A	ENST00000282344.6	-	7	1072	c.816A>T	c.(814-816)acA>acT	p.T272T		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	272	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.T272T(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AAGAGAGTTTTGTATATCGAT	0.358																																					Ovarian(37;808 911 7590 44442 44991)	ENST00000282344.6																			1	Substitution - coding silent(1)	p.T272T(1)	prostate(1)	breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						c.(814-816)acA>acT		ubiquitin specific peptidase 12							64.0	61.0	62.0					13																	27649444		2203	4300	6503	SO:0001819	synonymous_variant	219333				protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr13:27649444T>A	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"""Ubiquitin-specific peptidases"""	20485	protein-coding gene	gene with protein product			"""ubiquitin specific protease 12 like 1"", ""ubiquitin specific protease 12"""	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.816A>T	13.37:g.27649444T>A							p.T272T	NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)	7	1072	-		Lung SC(185;0.0161)	272					A8K0X0|Q5VZV3|Q8TC49	Silent	SNP	ENST00000282344.6	37	c.816A>T	CCDS31952.1																																																																																				0.358	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		42	61	0	0	0	0.819951	0	42	61				
DHX40	79665	broad.mit.edu	37	17	57679935	57679935	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:57679935G>A	ENST00000251241.4	+	15	2006	c.1859G>A	c.(1858-1860)cGa>cAa	p.R620Q	DHX40_ENST00000425628.3_Missense_Mutation_p.R543Q|DHX40_ENST00000451169.2_Missense_Mutation_p.R572Q	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	620							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.R620Q(3)		endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAAGTACTACGAAGATGTCTT	0.338																																						ENST00000451169.2																			3	Substitution - Missense(3)	p.R620Q(3)	prostate(2)|large_intestine(1)	endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20						c.(1714-1716)cGa>cAa		DEAH (Asp-Glu-Ala-His) box polypeptide 40							76.0	80.0	78.0					17																	57679935		2203	4300	6503	SO:0001583	missense	79665						ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr17:57679935G>A	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.1859G>A	17.37:g.57679935G>A	ENSP00000251241:p.Arg620Gln					DHX40_ENST00000251241.4_Missense_Mutation_p.R620Q|DHX40_ENST00000425628.3_Missense_Mutation_p.R543Q	p.R572Q			Q8IX18	DHX40_HUMAN			18	2074	+	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		620					B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Missense_Mutation	SNP	ENST00000251241.4	37	c.1715G>A	CCDS11617.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259773	0.95368	.	.	ENSG00000108406	ENST00000251241;ENST00000538926;ENST00000425628;ENST00000451169	T;T	0.04758	3.94;3.56	5.81	5.81	0.92471	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.22003	0.0530	M	0.71871	2.18	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.00035	-1.2262	10	0.34782	T	0.22	.	19.4253	0.94739	0.0:0.0:1.0:0.0	.	543;620	F5H625;Q8IX18	.;DHX40_HUMAN	Q	620;543;620;572	ENSP00000251241:R620Q;ENSP00000396039:R572Q	ENSP00000251241:R620Q	R	+	2	0	DHX40	55034717	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.709000	0.68384	2.906000	0.99361	0.655000	0.94253	CGA		0.338	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612		50	109	0	0	0	0.870114	0	50	109				
TRPM6	140803	broad.mit.edu	37	9	77448983	77448983	+	Missense_Mutation	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:77448983T>G	ENST00000360774.1	-	6	837	c.600A>C	c.(598-600)agA>agC	p.R200S	TRPM6_ENST00000359047.2_Missense_Mutation_p.R200S|TRPM6_ENST00000361255.3_Missense_Mutation_p.R195S|TRPM6_ENST00000449912.2_Missense_Mutation_p.R195S|TRPM6_ENST00000451710.3_Missense_Mutation_p.R200S|TRPM6_ENST00000376871.3_Missense_Mutation_p.R200S|TRPM6_ENST00000376864.4_Missense_Mutation_p.R200S|TRPM6_ENST00000376872.3_Missense_Mutation_p.R200S|TRPM6_ENST00000483186.1_5'Flank	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	200					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R200S(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TCCAGATTTTTCTCAAGGAAT	0.403																																						ENST00000451710.3																			1	Substitution - Missense(1)	p.R200S(1)	prostate(1)	NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						c.(598-600)agA>agC		transient receptor potential cation channel, subfamily M, member 6							136.0	126.0	130.0					9																	77448983		2203	4300	6503	SO:0001583	missense	140803				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr9:77448983T>G	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.600A>C	9.37:g.77448983T>G	ENSP00000354006:p.Arg200Ser					TRPM6_ENST00000360774.1_Missense_Mutation_p.R200S|TRPM6_ENST00000359047.2_Missense_Mutation_p.R200S|TRPM6_ENST00000449912.2_Missense_Mutation_p.R195S|TRPM6_ENST00000376871.3_Missense_Mutation_p.R200S|TRPM6_ENST00000376872.3_Missense_Mutation_p.R200S|TRPM6_ENST00000361255.3_Missense_Mutation_p.R195S|TRPM6_ENST00000376864.4_Missense_Mutation_p.R200S	p.R200S			Q9BX84	TRPM6_HUMAN			6	837	-			200					Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	c.600A>C	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.280894	0.40394	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.02067	4.47;4.47;4.47;4.47;4.47;4.47;4.47;4.47	5.69	0.662	0.17880	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	L	0.53249	1.67	0.47094	D	0.999317	B;B;B;B;B;B	0.22003	0.041;0.041;0.041;0.063;0.027;0.025	B;B;B;B;B;B	0.25405	0.011;0.011;0.011;0.049;0.06;0.037	T	0.49890	-0.8891	10	0.33141	T	0.24	.	5.1832	0.15171	0.1258:0.283:0.0:0.5912	.	200;200;200;200;200;195	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	S	200;200;200;200;195;195;199;200;200	ENSP00000354006:R200S;ENSP00000407341:R200S;ENSP00000366068:R200S;ENSP00000366067:R200S;ENSP00000396672:R195S;ENSP00000354962:R195S;ENSP00000366060:R200S;ENSP00000351942:R200S	ENSP00000351942:R200S	R	-	3	2	TRPM6	76638803	0.278000	0.24230	1.000000	0.80357	0.991000	0.79684	0.317000	0.19487	0.088000	0.17205	0.402000	0.26972	AGA		0.403	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		12	186	0	0	0	0.387290	0	12	186				
TTLL3	26140	broad.mit.edu	37	3	9870957	9870957	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:9870957C>A	ENST00000547186.1	+	10	1648	c.1432C>A	c.(1432-1434)Ccc>Acc	p.P478T	TTLL3_ENST00000426895.4_Missense_Mutation_p.P621T|TTLL3_ENST00000397241.1_Missense_Mutation_p.P266T|TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000427853.3_Missense_Mutation_p.P266T|ARPC4-TTLL3_ENST00000397256.1_Missense_Mutation_p.P539T|TTLL3_ENST00000430793.1_Missense_Mutation_p.P266T|TTLL3_ENST00000455274.1_Missense_Mutation_p.P266T|TTLL3_ENST00000383827.1_Missense_Mutation_p.P266T	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	478	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)	p.P478T(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					CACGATGGCACCCTCCACAGC	0.622																																						ENST00000383827.1																			1	Substitution - Missense(1)	p.P478T(1)	prostate(1)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26						c.(796-798)Ccc>Acc		tubulin tyrosine ligase-like family, member 3							70.0	66.0	67.0					3																	9870957		2203	4300	6503	SO:0001583	missense	26140				axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity	g.chr3:9870957C>A		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1432C>A	3.37:g.9870957C>A	ENSP00000446659:p.Pro478Thr					TTLL3_ENST00000427853.3_Missense_Mutation_p.P266T|TTLL3_ENST00000455274.1_Missense_Mutation_p.P266T|TTLL3_ENST00000547186.1_Missense_Mutation_p.P478T|TTLL3_ENST00000397241.1_Missense_Mutation_p.P266T|TTLL3_ENST00000426895.4_Missense_Mutation_p.P621T|TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000430793.1_Missense_Mutation_p.P266T|ARPC4-TTLL3_ENST00000397256.1_Missense_Mutation_p.P539T	p.P266T			Q9Y4R7	TTLL3_HUMAN			4	3077	+	Medulloblastoma(99;0.227)		478			TTL.		Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	37	c.796C>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.05|12.05	1.822439|1.822439	0.32237|0.32237	.|.	.|.	ENSG00000250151;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021;ENSG00000214021|ENSG00000214021	ENST00000397256;ENST00000426895;ENST00000547186;ENST00000397241;ENST00000427853;ENST00000443148;ENST00000383827;ENST00000455274;ENST00000430793|ENST00000310252	T;T;T;T;T;T;T;T;T|.	0.10192|.	2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9|.	5.03|5.03	5.03|5.03	0.67393|0.67393	.|.	0.253590|.	0.30800|.	U|.	0.008856|.	T|T	0.38453|0.38453	0.1041|0.1041	N|N	0.10945|0.10945	0.07|0.07	0.39105|0.39105	D|D	0.961365|0.961365	P;B;B;P;D;B|.	0.69078|.	0.616;0.22;0.34;0.621;0.997;0.372|.	P;B;B;P;D;B|.	0.67900|.	0.574;0.198;0.108;0.593;0.954;0.285|.	T|T	0.34825|0.34825	-0.9813|-0.9813	10|5	0.46703|.	T|.	0.11|.	.|.	13.3149|13.3149	0.60401|0.60401	0.0:0.7119:0.2881:0.0|0.0:0.7119:0.2881:0.0	.|.	417;266;266;478;539;266|.	B4DM47;Q9Y4R7-2;Q9Y4R7-5;Q9Y4R7;E7ETI0;C9JSD3|.	.;.;.;TTLL3_HUMAN;.;.|.	T|N	539;621;478;266;266;416;266;266;266|433	ENSP00000380427:P539T;ENSP00000392549:P621T;ENSP00000446659:P478T;ENSP00000380416:P266T;ENSP00000394462:P266T;ENSP00000398097:P416T;ENSP00000373338:P266T;ENSP00000409632:P266T;ENSP00000403874:P266T|.	ENSP00000380416:P266T|.	P|T	+|+	1|2	0|0	ARPC4-TTLL3;TTLL3|TTLL3	9845957|9845957	0.772000|0.772000	0.28567|0.28567	0.961000|0.961000	0.40146|0.40146	0.389000|0.389000	0.30415|0.30415	1.188000|1.188000	0.32102|0.32102	2.343000|2.343000	0.79666|0.79666	0.563000|0.563000	0.77884|0.77884	CCC|ACC		0.622	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		59	91	1	0	1.08141e-31	0.870114	1.42685e-31	59	91				
MARK3	4140	broad.mit.edu	37	14	103918266	103918266	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:103918266G>A	ENST00000429436.2	+	5	868	c.358G>A	c.(358-360)Gaa>Aaa	p.E120K	MARK3_ENST00000303622.9_Missense_Mutation_p.E120K|MARK3_ENST00000335102.5_Missense_Mutation_p.E120K|MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000416682.2_Missense_Mutation_p.E120K|MARK3_ENST00000216288.7_Missense_Mutation_p.E120K|MARK3_ENST00000440884.3_Missense_Mutation_p.E120K|MARK3_ENST00000553942.1_Missense_Mutation_p.E120K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E120K(4)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			GAAGTTATTCGAAGTCATTGA	0.353																																						ENST00000429436.2																			4	Substitution - Missense(4)	p.E120K(4)	prostate(2)|ovary(1)|large_intestine(1)	autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						c.(358-360)Gaa>Aaa		MAP/microtubule affinity-regulating kinase 3							171.0	168.0	169.0					14																	103918266		1851	4107	5958	SO:0001583	missense	4140						ATP binding|protein binding|protein serine/threonine kinase activity	g.chr14:103918266G>A	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.358G>A	14.37:g.103918266G>A	ENSP00000411397:p.Glu120Lys					MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000303622.9_Missense_Mutation_p.E120K|MARK3_ENST00000440884.3_Missense_Mutation_p.E120K|MARK3_ENST00000216288.7_Missense_Mutation_p.E120K|MARK3_ENST00000335102.5_Missense_Mutation_p.E120K|MARK3_ENST00000416682.2_Missense_Mutation_p.E120K|MARK3_ENST00000553942.1_Missense_Mutation_p.E120K	p.E120K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	Epithelial(46;0.241)		5	868	+		Melanoma(154;0.155)	120			Protein kinase.		O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	c.358G>A	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086533	0.76642	.	.	ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	T;T;T;T;T;T;T	0.26223	1.75;3.07;1.75;1.75;1.75;1.75;1.75	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.70108	2.13	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.87578	0.903;0.997;0.998;0.998;0.993;0.996	T	0.51957	-0.8639	10	0.72032	D	0.01	.	19.0276	0.92939	0.0:0.0:1.0:0.0	.	120;120;120;120;120;120	P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;MARK3_HUMAN;.;.;.	K	120	ENSP00000335347:E120K;ENSP00000402104:E120K;ENSP00000408092:E120K;ENSP00000411397:E120K;ENSP00000303698:E120K;ENSP00000216288:E120K;ENSP00000450772:E120K	ENSP00000216288:E120K	E	+	1	0	MARK3	102988019	1.000000	0.71417	0.999000	0.59377	0.020000	0.10135	8.655000	0.91098	2.797000	0.96272	0.563000	0.77884	GAA		0.353	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		26	337	0	0	0	0.693898	0	26	337				
A1BG	1	broad.mit.edu	37	19	58863782	58863782	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:58863782C>T	ENST00000263100.3	-	4	541	c.480G>A	c.(478-480)gaG>gaA	p.E160E	A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000593960.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	160	Ig-like V-type 2.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.E160E(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		CCTCAGGCACCTCCAGAAACT	0.627																																						ENST00000263100.3																			1	Substitution - coding silent(1)	p.E160E(1)	prostate(1)	NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15						c.(478-480)gaG>gaA		alpha-1-B glycoprotein							114.0	110.0	111.0					19																	58863782		2203	4300	6503	SO:0001819	synonymous_variant	1					extracellular region		g.chr19:58863782C>T		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.480G>A	19.37:g.58863782C>T						CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000599728.1_RNA	p.E160E	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)	4	541	-		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)	160			Ig-like V-type 2.		A8K052|Q68CK0|Q8IYJ6|Q96P39	Silent	SNP	ENST00000263100.3	37	c.480G>A	CCDS12976.1																																																																																				0.627	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786		12	207	0	0	0	0.435327	0	12	207				
METTL25	84190	broad.mit.edu	37	12	82792603	82792603	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:82792603C>A	ENST00000248306.3	+	4	630	c.561C>A	c.(559-561)taC>taA	p.Y187*	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	187							methyltransferase activity (GO:0008168)	p.Y187*(1)									GTAAAGGCTACCTAAGCTCTT	0.318																																						ENST00000248306.3																			1	Substitution - Nonsense(1)	p.Y187*(1)	prostate(1)								c.(559-561)taC>taA		methyltransferase like 25							39.0	40.0	40.0					12																	82792603		2203	4299	6502	SO:0001587	stop_gained	84190							g.chr12:82792603C>A	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.561C>A	12.37:g.82792603C>A	ENSP00000248306:p.Tyr187*					METTL25_ENST00000547357.1_3'UTR	p.Y187*	NM_032230.2	NP_115606.2					4	630	+								Q9H5Y3	Nonsense_Mutation	SNP	ENST00000248306.3	37	c.561C>A	CCDS9024.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.02|16.02	3.004457|3.004457	0.54254|0.54254	.|.	.|.	ENSG00000127720|ENSG00000127720	ENST00000550058|ENST00000248306;ENST00000548200	.|.	.|.	.|.	5.43|5.43	-0.443|-0.443	0.12249|0.12249	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.23766|.	0.0575|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41627|.	-0.9498|.	3|.	.|0.02654	.|T	.|1	-11.3673|-11.3673	12.1424|12.1424	0.54005|0.54005	0.0:0.5649:0.0:0.4351|0.0:0.5649:0.0:0.4351	.|.	.|.	.|.	.|.	N|X	146|187	.|.	.|ENSP00000248306:Y187X	T|Y	+|+	2|3	0|2	C12orf26|C12orf26	81316734|81316734	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.875000|0.875000	0.50365|0.50365	0.884000|0.884000	0.28214|0.28214	-0.263000|-0.263000	0.09378|0.09378	-1.974000|-1.974000	0.00461|0.00461	ACC|TAC		0.318	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		6	103	1	0	0.0293803	0.248553	0.032082	6	103				
SACM1L	22908	broad.mit.edu	37	3	45761023	45761023	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:45761023A>G	ENST00000389061.5	+	8	813	c.609A>G	c.(607-609)ggA>ggG	p.G203G	SACM1L_ENST00000541314.1_Silent_p.G142G|SACM1L_ENST00000418611.1_Silent_p.G100G	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	203	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.G203G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CTATTAATGGAAAATACTTTG	0.338																																						ENST00000389061.5																			1	Substitution - coding silent(1)	p.G203G(1)	prostate(1)	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23						c.(607-609)ggA>ggG		SAC1 suppressor of actin mutations 1-like (yeast)							112.0	111.0	111.0					3																	45761023		2203	4300	6503	SO:0001819	synonymous_variant	22908					Golgi apparatus		g.chr3:45761023A>G	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.609A>G	3.37:g.45761023A>G						SACM1L_ENST00000541314.1_Silent_p.G142G|SACM1L_ENST00000418611.1_Silent_p.G100G	p.G203G	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)	8	813	+			203			SAC.		A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Silent	SNP	ENST00000389061.5	37	c.609A>G	CCDS33745.1																																																																																				0.338	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		6	77	0	0	0	0.248553	0	6	77				
TJP1	7082	broad.mit.edu	37	15	30025006	30025006	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:30025006C>A	ENST00000346128.6	-	14	2224	c.1750G>T	c.(1750-1752)Gcc>Tcc	p.A584S	TJP1_ENST00000356107.6_Missense_Mutation_p.A584S|TJP1_ENST00000400011.2_Missense_Mutation_p.A588S|TJP1_ENST00000545208.2_Missense_Mutation_p.A584S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	584	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.A584S(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGTACACTGGCTAGCTGCTCA	0.403																																					Melanoma(77;681 1843 6309 6570)	ENST00000346128.6																			1	Substitution - Missense(1)	p.A584S(1)	prostate(1)	breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68						c.(1750-1752)Gcc>Tcc		tight junction protein 1							37.0	36.0	36.0					15																	30025006		1833	4089	5922	SO:0001583	missense	7082				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction		g.chr15:30025006C>A		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.1750G>T	15.37:g.30025006C>A	ENSP00000281537:p.Ala584Ser					TJP1_ENST00000356107.6_Missense_Mutation_p.A584S|TJP1_ENST00000400011.2_Missense_Mutation_p.A588S|TJP1_ENST00000545208.2_Missense_Mutation_p.A584S	p.A584S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)	14	2224	-		all_lung(180;7.48e-11)|Breast(32;0.000153)	584			SH3.		B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	c.1750G>T	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188857	0.57909	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.73	5.73	0.89815	Src homology-3 domain (2);	0.050125	0.85682	D	0.000000	T	0.35038	0.0918	M	0.88842	2.985	0.80722	D	1	B;B;B;B	0.24092	0.089;0.097;0.089;0.065	B;B;B;B	0.32393	0.088;0.144;0.145;0.073	T	0.18493	-1.0335	9	.	.	.	.	20.27	0.98469	0.0:1.0:0.0:0.0	.	577;584;584;588	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	584;588;584;584;584	ENSP00000281537:A584S;ENSP00000382890:A588S;ENSP00000441202:A584S;ENSP00000348416:A584S	.	A	-	1	0	TJP1	27812298	1.000000	0.71417	0.985000	0.45067	0.965000	0.64279	5.962000	0.70364	2.854000	0.98071	0.655000	0.94253	GCC		0.403	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		40	45	1	0	7.63091e-17	0.834066	9.53864e-17	40	45				
LOC220729	220729	broad.mit.edu	37	3	197348674	197348674	+	RNA	SNP	A	A	G	rs376114863		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:197348674A>G	ENST00000418868.1	-	0	585					NR_003266.2																						GGCTCTGTCCACCAAATGCAC	0.478																																						ENST00000418868.1																			0																																																			0							g.chr3:197348674A>G																													3.37:g.197348674A>G								NR_003266.2						0	585	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.478	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			5	203	0	0	0	0.184627	0	5	203				
ENPP7	339221	broad.mit.edu	37	17	77711840	77711840	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:77711840G>A	ENST00000328313.5	+	5	1593	c.1372G>A	c.(1372-1374)Gca>Aca	p.A458T		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7									p.A458T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTCTGAGGTCGCATAACGCCC	0.642																																						ENST00000328313.5																			1	Substitution - Missense(1)	p.A458T(1)	prostate(1)	breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34						c.(1372-1374)Gca>Aca		ectonucleotide pyrophosphatase/phosphodiesterase 7							79.0	71.0	74.0					17																	77711840		2203	4300	6503	SO:0001583	missense	339221				negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity	g.chr17:77711840G>A	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1372G>A	17.37:g.77711840G>A	ENSP00000332656:p.Ala458Thr						p.A458T	NM_178543.3	NP_848638.2	Q6UWV6	ENPP7_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)		5	1593	+			458						Missense_Mutation	SNP	ENST00000328313.5	37	c.1372G>A	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.338292	0.24253	.	.	ENSG00000182156	ENST00000328313	T	0.74632	-0.86	2.43	-4.66	0.03329	.	2.375630	0.02566	N	0.097348	T	0.47451	0.1446	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.20042	-1.0287	10	0.25751	T	0.34	.	0.6033	0.00748	0.3767:0.1725:0.2761:0.1747	.	458	Q6UWV6	ENPP7_HUMAN	T	458	ENSP00000332656:A458T	ENSP00000332656:A458T	A	+	1	0	ENPP7	75326435	0.000000	0.05858	0.010000	0.14722	0.041000	0.13682	-1.916000	0.01576	-1.087000	0.03081	-0.355000	0.07637	GCA		0.642	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		4	117	0	0	0	0.184627	0	4	117				
TECPR2	9895	broad.mit.edu	37	14	102891314	102891314	+	Splice_Site	SNP	A	A	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:102891314A>T	ENST00000359520.7	+	6	864		c.e6-1		TECPR2_ENST00000561228.1_Intron|TECPR2_ENST00000558678.1_Splice_Site	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2						autophagy (GO:0006914)|cell death (GO:0008219)			p.?(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						TTCTAATTTTAGTACTGGGAA	0.383																																						ENST00000359520.7																			1	Unknown(1)	p.?(1)	prostate(1)	breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						c.e6-1		tectonin beta-propeller repeat containing 2							65.0	75.0	71.0					14																	102891314		2196	4298	6494	SO:0001630	splice_region_variant	9895						protein binding	g.chr14:102891314A>T	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.639-1A>T	14.37:g.102891314A>T						TECPR2_ENST00000558678.1_Splice_Site|TECPR2_ENST00000561228.1_Intron		NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN			6	864	+								A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Splice_Site	SNP	ENST00000359520.7	37		CCDS32162.1	.	.	.	.	.	.	.	.	.	.	a	21.3	4.123248	0.77436	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0521	0.71881	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TECPR2	101961067	1.000000	0.71417	0.859000	0.33776	0.993000	0.82548	8.068000	0.89490	1.959000	0.56917	0.451000	0.29950	.		0.383	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	Intron	4	137	0	0	0	0.150653	0	4	137				
SGOL2	151246	broad.mit.edu	37	2	201436396	201436396	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:201436396A>G	ENST00000357799.4	+	7	1425	c.1327A>G	c.(1327-1329)Agg>Ggg	p.R443G		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	443					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.R443G(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GGATGGCAAAAGGGGTGCAGA	0.398																																						ENST00000357799.4																			1	Substitution - Missense(1)	p.R443G(1)	prostate(1)	NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						c.(1327-1329)Agg>Ggg		shugoshin-like 2 (S. pombe)							99.0	98.0	98.0					2																	201436396		1845	4081	5926	SO:0001583	missense	151246				cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding	g.chr2:201436396A>G	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1327A>G	2.37:g.201436396A>G	ENSP00000350447:p.Arg443Gly						p.R443G	NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN			7	1425	+			443					Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	c.1327A>G	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.112115	0.00353	.	.	ENSG00000163535	ENST00000357799	T	0.46451	0.87	5.15	-0.273	0.12915	.	0.879576	0.10046	N	0.722883	T	0.09992	0.0245	N	0.00210	-1.845	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35549	-0.9784	10	0.13853	T	0.58	1.345	8.5572	0.33489	0.3883:0.0:0.6117:0.0	.	443;443;443	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	G	443	ENSP00000350447:R443G	ENSP00000350447:R443G	R	+	1	2	SGOL2	201144641	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	0.281000	0.18810	0.047000	0.15862	0.477000	0.44152	AGG		0.398	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		3	263	0	0	0	0.150653	0	3	263				
DAK	26007	broad.mit.edu	37	11	61111398	61111398	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr11:61111398G>A	ENST00000394900.3	+	12	1282	c.1053G>A	c.(1051-1053)cgG>cgA	p.R351R		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	351					carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)	p.R351R(1)		NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						AGCGGAGCCGGGTAGCCCCTG	0.602																																						ENST00000394900.3																			1	Substitution - coding silent(1)	p.R351R(1)	prostate(1)	NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						c.(1051-1053)cgG>cgA		dihydroxyacetone kinase 2 homolog (S. cerevisiae)							46.0	55.0	52.0					11																	61111398		2203	4299	6502	SO:0001819	synonymous_variant	26007				glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding	g.chr11:61111398G>A		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"""dihydroxyacetone kinase 2 homolog (yeast)"""				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1053G>A	11.37:g.61111398G>A							p.R351R	NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN			12	1282	+			351					Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Silent	SNP	ENST00000394900.3	37	c.1053G>A	CCDS8003.1																																																																																				0.602	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		6	85	0	0	0	0.278610	0	6	85				
ARHGAP11B	89839	broad.mit.edu	37	15	30925726	30925726	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:30925726A>C	ENST00000428041.2	+	3	379	c.234A>C	c.(232-234)gaA>gaC	p.E78D		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	78	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.E78D(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CTTTAGAAGAACATATTCATA	0.373																																						ENST00000428041.2																			1	Substitution - Missense(1)	p.E78D(1)	prostate(1)	endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8						c.(232-234)gaA>gaC		Rho GTPase activating protein 11B							133.0	127.0	129.0					15																	30925726		2202	4300	6502	SO:0001583	missense	89839				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr15:30925726A>C	BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"""Rho GTPase activating proteins"""	15782	protein-coding gene	gene with protein product	"""GAP (1-8)"""		"""family with sequence similarity 7, member B1"""	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.234A>C	15.37:g.30925726A>C	ENSP00000392760:p.Glu78Asp						p.E78D	NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)	3	379	+		all_lung(180;2.71e-09)|Breast(32;0.00116)	78			Rho-GAP.			Missense_Mutation	SNP	ENST00000428041.2	37	c.234A>C	CCDS32185.1	.	.	.	.	.	.	.	.	.	.	.	7.909	0.736063	0.15574	.	.	ENSG00000187951	ENST00000428041	T	0.19394	2.15	1.8	-3.05	0.05396	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.293559	0.18664	U	0.134624	T	0.11239	0.0274	L	0.27944	0.81	0.21147	N	0.999777	B	0.17038	0.02	B	0.27608	0.081	T	0.37361	-0.9709	10	0.14656	T	0.56	.	7.3639	0.26762	0.4923:0.0:0.5077:0.0	.	78	Q3KRB8	RHGBB_HUMAN	D	78	ENSP00000392760:E78D	ENSP00000392760:E78D	E	+	3	2	ARHGAP11B	28713018	0.936000	0.31750	0.934000	0.37439	0.612000	0.37316	-0.091000	0.11146	-0.925000	0.03775	0.136000	0.15936	GAA		0.373	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841		4	186	0	0	0	0.150653	0	4	186				
PITPNC1	26207	broad.mit.edu	37	17	65688807	65688807	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:65688807G>A	ENST00000581322.1	+	9	802	c.802G>A	c.(802-804)Gtc>Atc	p.V268I	PITPNC1_ENST00000299954.9_3'UTR|PITPNC1_ENST00000335257.6_Missense_Mutation_p.V268I|PITPNC1_ENST00000580974.1_3'UTR			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	268					phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)	p.V268I(2)		breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GCCTTCTTCCGTCCGCAGTGC	0.557																																						ENST00000335257.6																			2	Substitution - Missense(2)	p.V268I(2)	prostate(1)|lung(1)	breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17						c.(802-804)Gtc>Atc		phosphatidylinositol transfer protein, cytoplasmic 1							121.0	127.0	125.0					17																	65688807		1991	4162	6153	SO:0001583	missense	26207				signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding	g.chr17:65688807G>A	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.802G>A	17.37:g.65688807G>A	ENSP00000464006:p.Val268Ile					PITPNC1_ENST00000580974.1_3'UTR|PITPNC1_ENST00000581322.1_Missense_Mutation_p.V268I|PITPNC1_ENST00000299954.9_3'UTR	p.V268I			Q9UKF7	PITC1_HUMAN	BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)		9	1149	+	all_cancers(12;3.03e-10)		268					A8K473|J3QR20|Q96I07	Missense_Mutation	SNP	ENST00000581322.1	37	c.802G>A	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	G	8.254	0.809691	0.16537	.	.	ENSG00000154217	ENST00000335257	T	0.44083	0.93	5.75	3.59	0.41128	.	0.222920	0.47455	D	0.000223	T	0.16811	0.0404	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05257	-1.0896	10	0.34782	T	0.22	-1.2887	4.3035	0.10935	0.3704:0.0:0.6296:0.0	.	268	Q9UKF7	PITC1_HUMAN	I	268	ENSP00000335618:V268I	ENSP00000335618:V268I	V	+	1	0	PITPNC1	63119269	1.000000	0.71417	0.882000	0.34594	0.097000	0.18754	4.034000	0.57289	1.451000	0.47736	-0.136000	0.14681	GTC		0.557	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417		34	153	0	0	0	0.769981	0	34	153				
ABCB4	5244	broad.mit.edu	37	7	87082328	87082328	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:87082328A>G	ENST00000265723.4	-	6	579	c.468T>C	c.(466-468)gcT>gcC	p.A156A	ABCB4_ENST00000545634.1_Silent_p.A156A|ABCB4_ENST00000453593.1_Silent_p.A156A|ABCB4_ENST00000359206.3_Silent_p.A156A|ABCB4_ENST00000358400.3_Silent_p.A156A	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	156	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.A156A(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	GTCGTAGAATAGCATGAAAAA	0.413																																						ENST00000265723.4																			1	Substitution - coding silent(1)	p.A156A(1)	prostate(1)	breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77						c.(466-468)gcT>gcC		ATP-binding cassette, sub-family B (MDR/TAP), member 4							120.0	109.0	113.0					7																	87082328		2203	4300	6503	SO:0001819	synonymous_variant	5244				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity	g.chr7:87082328A>G	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.468T>C	7.37:g.87082328A>G						ABCB4_ENST00000359206.3_Silent_p.A156A|ABCB4_ENST00000358400.3_Silent_p.A156A|ABCB4_ENST00000453593.1_Silent_p.A156A|ABCB4_ENST00000545634.1_Silent_p.A156A	p.A156A	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN			6	579	-	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)		156			ABC transmembrane type-1 1.		A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	c.468T>C	CCDS5606.1																																																																																				0.413	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		3	189	0	0	0	0.115264	0	3	189				
GBP2	2634	broad.mit.edu	37	1	89587611	89587611	+	Silent	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:89587611G>C	ENST00000370466.3	-	2	307	c.39C>G	c.(37-39)ctC>ctG	p.L13L	GBP2_ENST00000463660.1_5'Flank	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	13	GTPase domain (Globular). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L13L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TGTTATCAATGAGGCTCATTG	0.498																																						ENST00000370466.3																			1	Substitution - coding silent(1)	p.L13L(1)	prostate(1)	endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20						c.(37-39)ctC>ctG		guanylate binding protein 2, interferon-inducible							124.0	122.0	122.0					1																	89587611		2203	4300	6503	SO:0001819	synonymous_variant	2634				interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity	g.chr1:89587611G>C	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.39C>G	1.37:g.89587611G>C							p.L13L	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN		all cancers(265;0.0151)|Epithelial(280;0.0284)	2	307	-		Lung NSC(277;0.0908)	13					Q6GPH0|Q6IAU2|Q86TB0	Silent	SNP	ENST00000370466.3	37	c.39C>G	CCDS719.1																																																																																				0.498	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		5	252	0	0	0	0.184627	0	5	252				
ENTPD3-AS1	285266	broad.mit.edu	37	3	40418607	40418610	+	RNA	DEL	AGGA	AGGA	-	rs112497421		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:40418607_40418610delAGGA	ENST00000439293.1	-	0	143									ENTPD3 antisense RNA 1																		ggagggagggaggaaggaaggaag	0.554																																						ENST00000439293.1																			0																																																			0							g.chr3:40418607_40418610delAGGA			3p22.1	2012-10-12	2012-08-15		ENSG00000223797	ENSG00000223797		"""Long non-coding RNAs"""	26710	non-coding RNA	RNA, long non-coding			"""ENTPD3 antisense RNA 1 (non-protein coding)"""			12477932	Standard	NR_040100		Approved	FLJ36665	uc003cke.4		OTTHUMG00000156074		3.37:g.40418615_40418618delAGGA														0	143	-									RNA	DEL	ENST00000439293.1	37																																																																																						0.554	ENTPD3-AS1-002	KNOWN	basic	antisense	antisense	OTTHUMT00000342936.1	NR_040100		3	5						3	5	---	---	---	---
CTNNB1	1499	broad.mit.edu	37	3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	rs121913407		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CACAGCTCCTTCTCTGAGTGG	0.502		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)	ENST00000349496.5		15		Dom	yes		3	3p22-p21.3	1499	"""H, Mis, T"""	"""catenin (cadherin-associated protein), beta 1"""			"""E, M, O"""	PLAG1		"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""	CTNNB1/PLAG1(60)	355	Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7)	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	liver(151)|kidney(53)|soft_tissue(47)|large_intestine(37)|adrenal_gland(28)|endometrium(9)|stomach(7)|skin(6)|pituitary(3)|prostate(3)|thyroid(2)|small_intestine(2)|bone(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893						c.(133-135)Tct>Cct		catenin (cadherin-associated protein), beta 1, 88kDa	Lithium(DB01356)						84.0	74.0	78.0					3																	41266136		2203	4300	6503	SO:0001583	missense	1499	Pilomatrixoma, Familial Clustering of	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	g.chr3:41266136T>C	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.133T>C	3.37:g.41266136T>C	ENSP00000344456:p.Ser45Pro					CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P	p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	3	413	+			45		Missing (in colorectal cancer).|S -> F (in hepatocellular carcinoma).|S -> P (in hepatocellular carcinoma).			A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	37	c.133T>C	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440246	0.83993	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.65677	2.01	0.80722	D	1	D	0.60575	0.988	P	0.62649	0.905	T	0.69083	-0.5239	10	0.87932	D	0	-13.6823	16.3453	0.83126	0.0:0.0:0.0:1.0	.	45	P35222	CTNB1_HUMAN	P	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P	ENSP00000344456:S45P	S	+	1	0	CTNNB1	41241140	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	TCT		0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		5	105	0	0	0	0.184627	0	5	105				
CASC6	101929083	broad.mit.edu	37	6	92356678	92356679	+	lincRNA	DEL	AA	AA	-	rs56890015|rs369105287	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:92356678_92356679delAA	ENST00000437768.1	-	0	263					NR_104154.1				cancer susceptibility candidate 6 (non-protein coding)																		aattttagccAAAAAAAAAAAA	0.337																																						ENST00000437768.1																			0																																																			0							g.chr6:92356678_92356679delAA	BC037927		6q15	2013-08-22			ENSG00000224944	ENSG00000224944		"""Long non-coding RNAs"""	49076	non-coding RNA	RNA, long non-coding							Standard	NR_104154		Approved				OTTHUMG00000015221		6.37:g.92356688_92356689delAA														0	263	-									RNA	DEL	ENST00000437768.1	37																																																																																						0.337	CASC6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000041538.1			5	6						5	6	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151853293	151853293	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151853293delC	ENST00000262189.6	-	45	12027	c.11809delG	c.(11809-11811)gaafs	p.E3937fs	KMT2C_ENST00000485241.1_5'Flank|KMT2C_ENST00000355193.2_Frame_Shift_Del_p.E3994fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3937					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)										ATCATACCTTCATGGCTCACT	0.438																																						ENST00000355193.2																			0											c.(11980-11982)aafs		lysine (K)-specific methyltransferase 2C							137.0	140.0	139.0					7																	151853293		2203	4300	6503	SO:0001589	frameshift_variant	58508							g.chr7:151853293delC	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.11809delG	7.37:g.151853293delC	ENSP00000262189:p.Glu3937fs					KMT2C_ENST00000262189.6_Frame_Shift_Del_p.E3937fs	p.E3994fs							46	12198	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	c.11980delG	CCDS5931.1																																																																																				0.438	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			22	271						22	271	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151859486	151859487	+	Frame_Shift_Ins	INS	-	-	TT			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151859486_151859487insTT	ENST00000262189.6	-	43	11393_11394	c.11175_11176insAA	c.(11173-11178)acagagfs	p.E3726fs	KMT2C_ENST00000355193.2_Frame_Shift_Ins_p.E3726fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3726					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)										GGGCAGGACTCTGTCTCAGCCT	0.48																																						ENST00000355193.2																			0											c.(11173-11178)acagtcfs		lysine (K)-specific methyltransferase 2C																																				SO:0001589	frameshift_variant	58508							g.chr7:151859486_151859487insTT	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.11175_11176insAA	7.37:g.151859486_151859487insTT	ENSP00000262189:p.Glu3726fs					KMT2C_ENST00000262189.6_Frame_Shift_Ins_p.V3726fs	p.V3726fs							43	11393_11394	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Ins	INS	ENST00000262189.6	37	c.11175_11176insAA	CCDS5931.1																																																																																				0.480	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			196	453						196	453	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151873437	151873437	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151873437delG	ENST00000262189.6	-	38	9319	c.9101delC	c.(9100-9102)cctfs	p.P3034fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.P3034fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3034	Gln-rich.				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)										TAATGTTTGAGGAATCATTAG	0.473																																						ENST00000355193.2																			0											c.(9100-9102)ctfs		lysine (K)-specific methyltransferase 2C							129.0	121.0	124.0					7																	151873437		2203	4300	6503	SO:0001589	frameshift_variant	58508							g.chr7:151873437delG	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.9101delC	7.37:g.151873437delG	ENSP00000262189:p.Pro3034fs					KMT2C_ENST00000262189.6_Frame_Shift_Del_p.P3034fs	p.P3034fs							38	9319	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	c.9101delC	CCDS5931.1																																																																																				0.473	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			61	145						61	145	---	---	---	---
DSCC1	79075	broad.mit.edu	37	8	120850633	120850638	+	In_Frame_Del	DEL	CACCAG	CACCAG	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:120850633_120850638delCACCAG	ENST00000313655.4	-	8	1148_1153	c.934_939delCTGGTG	c.(934-939)ctggtgdel	p.LV312del		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	312					DNA replication (GO:0006260)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGTGTCTATCCACCAGCGCTAAACCC	0.364																																						ENST00000313655.4																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9						c.(934-939)del		DNA replication and sister chromatid cohesion 1																																				SO:0001651	inframe_deletion	79075				DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding	g.chr8:120850633_120850638delCACCAG		CCDS6330.1	8q24.12	2013-05-24	2013-05-24		ENSG00000136982	ENSG00000136982			24453	protein-coding gene	gene with protein product	"""defective in sister chromatid cohesion homolog 1 (S. cerevisiae)"""	613203	"""defective in sister chromatid cohesion 1 homolog (S. cerevisiae)"""			12766176, 20826785	Standard	NM_024094		Approved	DCC1, hDCC1, MGC5528	uc003yov.3	Q9BVC3	OTTHUMG00000165010	ENST00000313655.4:c.934_939delCTGGTG	8.37:g.120850633_120850638delCACCAG	ENSP00000322180:p.Leu312_Val313del						p.LV312del	NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	STAD - Stomach adenocarcinoma(47;0.00185)		8	1148_1153	-	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		312					Q969N5	In_Frame_Del	DEL	ENST00000313655.4	37	c.934_939delCTGGTG	CCDS6330.1																																																																																				0.364	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094		47	170						47	170	---	---	---	---
CYC1	1537	broad.mit.edu	37	8	145151373	145151373	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:145151373delA	ENST00000318911.4	+	4	660	c.587delA	c.(586-588)gacfs	p.D196fs		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	196	Cytochrome c.				cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGCCCCCTGACCTCAGCTAC	0.577											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000318911.4																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15						c.(586-588)gcfs		cytochrome c-1							115.0	109.0	111.0					8																	145151373		2203	4300	6503	SO:0001589	frameshift_variant	1537				respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding	g.chr8:145151373delA	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"""Mitochondrial respiratory chain complex / Complex III"""	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.587delA	8.37:g.145151373delA	ENSP00000317159:p.Asp196fs		OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1692		p.D196fs	NM_001916.3	NP_001907.2	P08574	CY1_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		4	660	+	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		196			Cytochrome c.		Q5U062|Q6FHS7	Frame_Shift_Del	DEL	ENST00000318911.4	37	c.587delA	CCDS6415.1																																																																																				0.577	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916		20	145						20	145	---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114489999	114490000	+	Frame_Shift_Ins	INS	-	-	CCAAA			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:114489999_114490000insCCAAA	ENST00000318737.4	-	11	1683_1684	c.1555_1556insTTTGG	c.(1555-1557)gacfs	p.D519fs	C9orf84_ENST00000394777.4_Frame_Shift_Ins_p.D480fs|C9orf84_ENST00000394779.3_Frame_Shift_Ins_p.D480fs|C9orf84_ENST00000374287.3_Frame_Shift_Ins_p.D519fs	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	519										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GCTCAAAAGGTCCAAATCATTC	0.332																																						ENST00000394779.3																			0				breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						c.(1438-1440)cctfs		chromosome 9 open reading frame 84																																				SO:0001589	frameshift_variant	158401							g.chr9:114489999_114490000insCCAAA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1551_1555dupTTTGG	9.37:g.114490000_114490004dupCCAAA	ENSP00000322108:p.Asp519fs					C9orf84_ENST00000374287.3_Frame_Shift_Ins_p.P519fs|C9orf84_ENST00000394777.4_Frame_Shift_Ins_p.P480fs|C9orf84_ENST00000318737.4_Frame_Shift_Ins_p.P519fs	p.P480fs	NM_001080551.1	NP_001074020.1	Q5VXU9	CI084_HUMAN			9	1682_1683	-			519					A2A2V3|Q2M1H8|Q96M73	Frame_Shift_Ins	INS	ENST00000318737.4	37	c.1438_1439insTTTGG	CCDS6781.3																																																																																				0.332	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		22	326						22	326	---	---	---	---
CDKN1B	1027	broad.mit.edu	37	12	12870803	12870803	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:12870803delC	ENST00000228872.4	+	1	746	c.30delC	c.(28-30)agcfs	p.S10fs	CDKN1B_ENST00000396340.1_Frame_Shift_Del_p.S10fs|CDKN1B_ENST00000477087.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	10					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CTAACGGGAGCCCTAGCCTGG	0.607																																						ENST00000228872.4																			0				breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13						c.(28-30)agfs		cyclin-dependent kinase inhibitor 1B (p27, Kip1)							39.0	48.0	45.0					12																	12870803		2203	4297	6500	SO:0001589	frameshift_variant	1027				autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle	cytosol|endosome|nucleoplasm	cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity	g.chr12:12870803delC	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.30delC	12.37:g.12870803delC	ENSP00000228872:p.Ser10fs					CDKN1B_ENST00000477087.1_Intron|CDKN1B_ENST00000396340.1_Frame_Shift_Del_p.S10fs	p.S10fs	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN		BRCA - Breast invasive adenocarcinoma(232;0.0336)	1	746	+		Prostate(47;0.0322)|all_epithelial(100;0.159)	10					Q16307|Q5U0H2|Q9BUS6	Frame_Shift_Del	DEL	ENST00000228872.4	37	c.30delC	CCDS8653.1																																																																																				0.607	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064		10	77						10	77	---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46246234	46246241	+	Frame_Shift_Del	DEL	GTGGTACT	GTGGTACT	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:46246234_46246241delGTGGTACT	ENST00000334344.6	+	15	4500_4507	c.4328_4335delGTGGTACT	c.(4327-4335)agtggtactfs	p.SGT1443fs	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_Frame_Shift_Del_p.SGT51fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.SGT1053fs|ARID2_ENST00000422737.1_Frame_Shift_Del_p.SGT1294fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1443					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAGCAATTTAGTGGTACTGATTTGCTTA	0.418			"""N, S, F"""		hepatocellular carcinoma																																	ENST00000334344.6				Rec	yes		12	12q12	196528	"""N, S, F"""	AT rich interactive domain 2			E			hepatocellular carcinoma		0				NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116						c.(4327-4335)afs		AT rich interactive domain 2 (ARID, RFX-like)																																				SO:0001589	frameshift_variant	196528				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding	g.chr12:46246234_46246241delGTGGTACT		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4328_4335delGTGGTACT	12.37:g.46246234_46246241delGTGGTACT	ENSP00000335044:p.Ser1443fs					ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Frame_Shift_Del_p.SGT1294fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.SGT1053fs|ARID2_ENST00000457135.1_Frame_Shift_Del_p.SGT51fs	p.SGT1443fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)	15	4500_4507	+	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	1443					Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	37	c.4328_4335delGTGGTACT	CCDS31783.1																																																																																				0.418	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		67	315						67	315	---	---	---	---
RP11-116N8.1	0	broad.mit.edu	37	14	36463290	36463291	+	RNA	INS	-	-	TCCT	rs66569553|rs377264324|rs545267192	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:36463290_36463291insTCCT	ENST00000550089.1	+	0	242																											GACCATATTTAtccttccttcc	0.366														2982	0.595447	0.6241	0.4769	5008	,	,		21371	0.7748		0.4026	False		,,,				2504	0.6544					ENST00000550089.1																			0																																																			0							g.chr14:36463290_36463291insTCCT																													14.37:g.36463295_36463298dupTCCT														0	242	+									RNA	INS	ENST00000550089.1	37																																																																																						0.366	RP11-116N8.1-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000409615.1			3	3						3	3	---	---	---	---
CCDC144NL	339184	broad.mit.edu	37	17	20768756	20768756	+	Frame_Shift_Del	DEL	T	T	-	rs139187048		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:20768756delT	ENST00000327925.5	-	4	757	c.638delA	c.(637-639)aagfs	p.K213fs	RP11-344E13.3_ENST00000577537.1_RNA|CCDC144NL_ENST00000539484.1_5'UTR	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	213										large_intestine(3)|lung(3)|skin(1)	7						CACATGATTCTTCCCCTTTCT	0.368																																						ENST00000327925.5																			0				large_intestine(3)|lung(3)|skin(1)	7						c.(637-639)agfs		coiled-coil domain containing 144 family, N-terminal like							103.0	95.0	98.0					17																	20768756		2203	4300	6503	SO:0001589	frameshift_variant	339184							g.chr17:20768756delT		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.638delA	17.37:g.20768756delT	ENSP00000328054:p.Lys213fs					CCDC144NL_ENST00000539484.1_5'UTR	p.K213fs	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN			4	757	-			213						Frame_Shift_Del	DEL	ENST00000327925.5	37	c.638delA	CCDS32591.1																																																																																				0.368	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306		7	162						7	162	---	---	---	---
