#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_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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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	t_alt_count	t_ref_count
ANKRD26	22852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	27381396	27381396	+	Missense_Mutation	SNP	G	G	C			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr10:27381396G>C	ENST00000376087.4	-	4	742	c.577C>G	c.(577-579)Caa>Gaa	p.Q193E	ANKRD26_ENST00000436985.2_Missense_Mutation_p.Q193E	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	193					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCCACCATTTGCTGCTTTTTT	0.323																																																0													91.0	87.0	88.0					10																	27381396		1808	4074	5882	SO:0001583	missense	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.577C>G	10.37:g.27381396G>C	ENSP00000365255:p.Gln193Glu		A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	.	.	.	.	.	.	.	.	.	.	G	0.142	-1.101452	0.01828	.	.	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.61158	0.13;0.13	4.29	-8.59	0.00893	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.19248	0.0462	N	0.00778	-1.195	0.19575	N	0.999963	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42766	-0.9432	9	0.09590	T	0.72	.	11.428	0.50022	0.0:0.5585:0.1863:0.2552	.	193;193	Q9UPS8-3;Q9UPS8	.;ANR26_HUMAN	E	193	ENSP00000365255:Q193E;ENSP00000405112:Q193E	ENSP00000365255:Q193E	Q	-	1	0	ANKRD26	27421402	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.390000	0.20768	-1.503000	0.01812	-0.282000	0.10007	CAA		0.323	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			7	28	7	28
TLL2	7093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	98144479	98144479	+	Missense_Mutation	SNP	C	C	T	rs141438733		TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr10:98144479C>T	ENST00000357947.3	-	16	2284	c.2059G>A	c.(2059-2061)Gac>Aac	p.D687N		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	687	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AGCTTGGCGTCGGGGGACAGG	0.622																																																0								C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	115.0	110.0	112.0		2059	4.6	0.9	10	dbSNP_134	112	0,8600		0,0,4300	no	missense	TLL2	NM_012465.3	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	687/1016	98144479	1,13005	2203	4300	6503	SO:0001583	missense	7093			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2059G>A	10.37:g.98144479C>T	ENSP00000350630:p.Asp687Asn		A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252929	0.80135	2.27E-4	0.0	ENSG00000095587	ENST00000357947	T	0.18016	2.24	4.59	4.59	0.56863	CUB (5);	0.000000	0.47455	D	0.000234	T	0.24236	0.0587	N	0.25825	0.765	0.58432	D	0.999996	D	0.71674	0.998	D	0.65443	0.935	T	0.01657	-1.1302	10	0.07644	T	0.81	.	16.9266	0.86178	0.0:1.0:0.0:0.0	.	687	Q9Y6L7	TLL2_HUMAN	N	687	ENSP00000350630:D687N	ENSP00000350630:D687N	D	-	1	0	TLL2	98134469	1.000000	0.71417	0.852000	0.33557	0.893000	0.52053	5.854000	0.69503	2.548000	0.85928	0.484000	0.47621	GAC		0.622	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			73	114	73	114
MGEA5	10724	hgsc.bcm.edu;broad.mit.edu	37	10	103577687	103577687	+	Silent	SNP	C	C	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr10:103577687C>A	ENST00000361464.3	-	1	488	c.93G>T	c.(91-93)ccG>ccT	p.P31P	MGEA5_ENST00000419011.2_Silent_p.P31P|MGEA5_ENST00000370094.3_Silent_p.P31P|KCNIP2-AS1_ENST00000412353.1_RNA|MGEA5_ENST00000357797.5_Silent_p.P31P|MGEA5_ENST00000439817.1_Silent_p.P31P	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	31					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GAGCTGCCGGCGGCTCCAGCG	0.726																																																0													6.0	8.0	7.0					10																	103577687		2142	4182	6324	SO:0001819	synonymous_variant	10724			AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"""nuclear cytoplasmic O-GlcNAcase and acetyltransferase"""	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.93G>T	10.37:g.103577687C>A			B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	37	CCDS7520.1																																																																																				0.726	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		8	7	8	7
CUEDC2	79004	hgsc.bcm.edu;broad.mit.edu	37	10	104184887	104184887	+	Missense_Mutation	SNP	G	G	A	rs562865002	byFrequency	TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr10:104184887G>A	ENST00000369937.4	-	2	204	c.59C>T	c.(58-60)cCg>cTg	p.P20L	CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	20						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GTCGGCCTCCGGGAGGTGTGT	0.602													G|||	2	0.000399361	0.0008	0.0	5008	,	,		14555	0.001		0.0	False		,,,				2504	0.0															0													53.0	56.0	55.0					10																	104184887		2029	4183	6212	SO:0001583	missense	79004			BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"""chromosome 10 open reading frame 66"""	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.59C>T	10.37:g.104184887G>A	ENSP00000358953:p.Pro20Leu		D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	37	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.919149	0.73098	.	.	ENSG00000107874	ENST00000369937	D	0.86366	-2.11	5.3	2.32	0.28847	.	0.000000	0.85682	D	0.000000	D	0.88047	0.6332	L	0.41492	1.28	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.86216	0.1628	10	0.72032	D	0.01	-6.4559	7.533	0.27693	0.1546:0.1364:0.709:0.0	.	20	Q9H467	CUED2_HUMAN	L	20	ENSP00000358953:P20L	ENSP00000358953:P20L	P	-	2	0	CUEDC2	104174877	1.000000	0.71417	0.997000	0.53966	0.955000	0.61496	7.663000	0.83820	0.629000	0.30376	-0.266000	0.10368	CCG		0.602	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040		6	84	6	84
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	1087506	1087506	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr11:1087506G>A	ENST00000441003.2	+	24	3284	c.3257G>A	c.(3256-3258)gGg>gAg	p.G1086E	MUC2_ENST00000359061.5_Missense_Mutation_p.G1086E	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1086					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GACACGGGTGGGGACTGTGAG	0.652																																																0													81.0	92.0	88.0					11																	1087506		2164	4264	6428	SO:0001583	missense	4583			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3257G>A	11.37:g.1087506G>A	ENSP00000415183:p.Gly1086Glu		Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	g	16.92	3.255175	0.59321	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.18960	2.18;2.22	3.62	3.62	0.41486	.	0.177197	0.33834	U	0.004513	T	0.51618	0.1685	M	0.87900	2.915	0.50171	D	0.999855	D	0.89917	1.0	D	0.97110	1.0	T	0.64326	-0.6434	10	0.87932	D	0	.	15.867	0.79071	0.0:0.0:1.0:0.0	.	1086	E7EUV1	.	E	1086	ENSP00000415183:G1086E;ENSP00000351956:G1086E	ENSP00000351956:G1086E	G	+	2	0	MUC2	1077506	1.000000	0.71417	0.257000	0.24404	0.883000	0.51084	7.548000	0.82154	2.028000	0.59812	0.479000	0.44913	GGG		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		15	31	15	31
OR5D18	219438	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55587473	55587473	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr11:55587473G>A	ENST00000333976.4	+	1	388	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				GCCTATGACCGCTTCGTGGCC	0.458																																																0													173.0	165.0	168.0					11																	55587473		2200	4296	6496	SO:0001583	missense	219438			AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.368G>A	11.37:g.55587473G>A	ENSP00000335025:p.Arg123His		Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	16.16	3.044498	0.55110	.	.	ENSG00000186119	ENST00000333976	T	0.77489	-1.1	4.84	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38663	N	0.001602	T	0.77751	0.4177	M	0.85630	2.765	0.34540	D	0.710111	B	0.29716	0.255	B	0.24006	0.05	T	0.82983	-0.0186	10	0.66056	D	0.02	-3.2743	11.5101	0.50488	0.0934:0.0:0.9066:0.0	.	123	Q8NGL1	OR5DI_HUMAN	H	123	ENSP00000335025:R123H	ENSP00000335025:R123H	R	+	2	0	OR5D18	55344049	0.252000	0.23972	0.617000	0.29091	0.780000	0.44128	2.570000	0.45981	1.148000	0.42385	0.560000	0.71715	CGC		0.458	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		44	143	44	143
INPPL1	3636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	71942617	71942617	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr11:71942617G>A	ENST00000298229.2	+	13	1777	c.1573G>A	c.(1573-1575)Gtc>Atc	p.V525I	INPPL1_ENST00000541756.1_Missense_Mutation_p.V283I|INPPL1_ENST00000538751.1_Missense_Mutation_p.V283I	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	525					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TATCAGCCATGTCAGTACGTC	0.562																																																0													141.0	105.0	117.0					11																	71942617		2200	4293	6493	SO:0001583	missense	3636			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.1573G>A	11.37:g.71942617G>A	ENSP00000298229:p.Val525Ile		B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.079094	0.76528	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751	D;D;D	0.95482	-3.72;-3.72;-3.72	5.81	5.81	0.92471	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.92675	0.7672	N	0.21508	0.67	0.51767	D	0.999937	P	0.49696	0.927	P	0.47015	0.534	D	0.91356	0.5108	10	0.25106	T	0.35	.	17.5764	0.87950	0.0:0.0:1.0:0.0	.	525	O15357	SHIP2_HUMAN	I	525;283;283	ENSP00000298229:V525I;ENSP00000446360:V283I;ENSP00000444619:V283I	ENSP00000298229:V525I	V	+	1	0	INPPL1	71620265	1.000000	0.71417	0.978000	0.43139	0.989000	0.77384	4.623000	0.61247	2.746000	0.94184	0.655000	0.94253	GTC		0.562	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		32	73	32	73
C12orf50	160419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	88390403	88390403	+	Missense_Mutation	SNP	T	T	C			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr12:88390403T>C	ENST00000298699.2	-	5	490	c.310A>G	c.(310-312)Aag>Gag	p.K104E	C12orf50_ENST00000550553.1_Missense_Mutation_p.K104E	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	104										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						TCAGGGGTCTTTGTCCATAAA	0.289																																																0													86.0	90.0	89.0					12																	88390403		2199	4295	6494	SO:0001583	missense	0			AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.310A>G	12.37:g.88390403T>C	ENSP00000298699:p.Lys104Glu		Q6P674	Missense_Mutation	SNP	ENST00000298699.2	37	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.218919	0.79464	.	.	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944	T;T	0.44083	0.93;0.98	5.18	5.18	0.71444	.	0.087723	0.49305	D	0.000149	T	0.61489	0.2351	M	0.75447	2.3	0.33598	D	0.601967	D;D	0.69078	0.997;0.986	D;P	0.66196	0.942;0.84	T	0.74627	-0.3602	10	0.56958	D	0.05	.	12.5481	0.56212	0.0:0.0:0.0:1.0	.	158;104	G3V208;Q8NA57	.;CL050_HUMAN	E	104;104;158	ENSP00000298699:K104E;ENSP00000448344:K104E	ENSP00000298699:K104E	K	-	1	0	C12orf50	86914534	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.529000	0.60588	1.938000	0.56188	0.460000	0.39030	AAG		0.289	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589		10	59	10	59
GPR180	160897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	95273351	95273351	+	Silent	SNP	A	A	G			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr13:95273351A>G	ENST00000376958.4	+	6	781	c.756A>G	c.(754-756)caA>caG	p.Q252Q		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	252					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					TCGCTTCCCAAATTCAGATGT	0.373																																																0													138.0	129.0	132.0					13																	95273351		2203	4300	6503	SO:0001819	synonymous_variant	160897			AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"""intimal thickness related receptor"""	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.756A>G	13.37:g.95273351A>G			A8K1D5	Silent	SNP	ENST00000376958.4	37	CCDS9472.1																																																																																				0.373	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989		12	51	12	51
HEATR5A	25938	hgsc.bcm.edu;ucsc.edu	37	14	31833463	31833463	+	Missense_Mutation	SNP	G	G	A	rs201317895		TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr14:31833463G>A	ENST00000389961.3	-	13	1984	c.1985C>T	c.(1984-1986)aCa>aTa	p.T662I	HEATR5A_ENST00000543095.2_Missense_Mutation_p.T668I|HEATR5A_ENST00000439348.1_Missense_Mutation_p.T662I|HEATR5A_ENST00000439727.1_Missense_Mutation_p.T375I|HEATR5A_ENST00000404677.3_Missense_Mutation_p.T668I			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	662										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		CACTGACGGTGTTTTCAAAGG	0.294																																																0								G	ILE/THR	0,3636		0,0,1818	54.0	50.0	51.0		2003	2.2	1.0	14		51	4,8118		0,4,4057	yes	missense	HEATR5A	NM_015473.3	89	0,4,5875	AA,AG,GG		0.0492,0.0,0.034	benign	668/2047	31833463	4,11754	1818	4061	5879	SO:0001583	missense	25938			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1985C>T	14.37:g.31833463G>A	ENSP00000374611:p.Thr662Ile		Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.709343|2.709343	0.48517|0.48517	0.0|0.0	4.92E-4|4.92E-4	ENSG00000129493|ENSG00000129493	ENST00000538864|ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677	.|T;T;T;T;T	.|0.66099	.|-0.19;-0.19;-0.19;-0.19;-0.19	5.41|5.41	2.21|2.21	0.28008|0.28008	.|Armadillo-type fold (1);	.|0.380726	.|0.28828	.|N	.|0.014002	T|T	0.52468|0.52468	0.1736|0.1736	L|L	0.43152|0.43152	1.355|1.355	0.34967|0.34967	D|D	0.752782|0.752782	.|B;B;B	.|0.27853	.|0.191;0.027;0.12	.|B;B;B	.|0.29942	.|0.109;0.043;0.054	T|T	0.57785|0.57785	-0.7751|-0.7751	5|10	.|0.87932	.|D	.|0	.|.	9.5878|9.5878	0.39528|0.39528	0.2562:0.0:0.7438:0.0|0.2562:0.0:0.7438:0.0	.|.	.|668;662;662	.|B5MC49;Q86XA9-2;Q86XA9	.|.;.;HTR5A_HUMAN	Y|I	296|662;662;375;668;668	.|ENSP00000374611:T662I;ENSP00000405407:T662I;ENSP00000408681:T375I;ENSP00000437968:T668I;ENSP00000384646:T668I	.|ENSP00000374611:T662I	H|T	-|-	1|2	0|0	HEATR5A|HEATR5A	30903214|30903214	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.995000|0.995000	0.86356|0.86356	3.860000|3.860000	0.55995|0.55995	0.121000|0.121000	0.18284|0.18284	0.563000|0.563000	0.77884|0.77884	CAC|ACA		0.294	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		7	3	7	3
SEL1L	6400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	81946063	81946063	+	Missense_Mutation	SNP	A	A	C			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr14:81946063A>C	ENST00000336735.4	-	20	2184	c.2068T>G	c.(2068-2070)Ttt>Gtt	p.F690V		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	690	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		ATGTCATAAAAACGTTTCGCA	0.383																																																0													78.0	78.0	78.0					14																	81946063		2203	4300	6503	SO:0001583	missense	6400				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.2068T>G	14.37:g.81946063A>C	ENSP00000337053:p.Phe690Val		Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	37	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	A	34	5.294966	0.95546	.	.	ENSG00000071537	ENST00000336735;ENST00000261258	T	0.54479	0.57	6.04	6.04	0.98038	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.66848	0.2831	L	0.54323	1.7	0.80722	D	1	P	0.52316	0.952	P	0.60541	0.876	T	0.68307	-0.5443	10	0.66056	D	0.02	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	690	Q9UBV2	SE1L1_HUMAN	V	690;51	ENSP00000337053:F690V	ENSP00000261258:F51V	F	-	1	0	SEL1L	81015816	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.890000	0.92477	2.317000	0.78254	0.460000	0.39030	TTT		0.383	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		11	62	11	62
ABCA3	21	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	2374516	2374516	+	Silent	SNP	G	G	A	rs138952710	byFrequency	TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr16:2374516G>A	ENST00000301732.5	-	6	1036	c.336C>T	c.(334-336)tcC>tcT	p.S112S	ABCA3_ENST00000382381.3_Silent_p.S112S|ABCA3_ENST00000567910.1_Silent_p.S112S	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	112					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	AGTCCTTCTCGGAGGGAAAGC	0.587													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18653	0.0		0.0	False		,,,				2504	0.0															0													55.0	47.0	49.0					16																	2374516		2198	4300	6498	SO:0001819	synonymous_variant	21			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.336C>T	16.37:g.2374516G>A			B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																				0.587	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		26	53	26	53
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	27100381	27100381	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr1:27100381C>T	ENST00000324856.7	+	17	4464	c.4093C>T	c.(4093-4095)Caa>Taa	p.Q1365*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q982*|ARID1A_ENST00000540690.1_5'UTR|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1365*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1365	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GTATCAACAGCAACAGCAGGT	0.498			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0													125.0	129.0	128.0					1																	27100381		2203	4300	6503	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4093C>T	1.37:g.27100381C>T	ENSP00000320485:p.Gln1365*		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.553595|9.553595	0.99202|0.99202	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152	.|.	.|.	.|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.78515|.	0.4295|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.79401|.	-0.1819|.	4|.	.|0.62326	.|D	.|0.03	-6.357|-6.357	19.7727|19.7727	0.96373|0.96373	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|X	261|1365;1365;982	.|.	.|ENSP00000320485:Q1365X	A|Q	+|+	2|1	0|0	ARID1A|ARID1A	26972968|26972968	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.914000|0.914000	0.54420|0.54420	7.487000|7.487000	0.81328|0.81328	2.688000|2.688000	0.91661|0.91661	0.655000|0.655000	0.94253|0.94253	GCA|CAA		0.498	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		63	109	63	109
TRMT13	54482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	100613719	100613719	+	Missense_Mutation	SNP	T	T	G			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr1:100613719T>G	ENST00000370141.2	+	10	1093	c.1087T>G	c.(1087-1089)Tat>Gat	p.Y363D		NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	363					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GGAATTCCATTATTTCCAGCG	0.428																																																0													107.0	100.0	102.0					1																	100613719		2203	4300	6503	SO:0001583	missense	54482			BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.1087T>G	1.37:g.100613719T>G	ENSP00000359160:p.Tyr363Asp		Q5VVL0|Q9NW65	Missense_Mutation	SNP	ENST00000370141.2	37	CCDS765.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.165963	0.57476	.	.	ENSG00000122435	ENST00000370141	T	0.43688	0.94	5.75	5.75	0.90469	Methyltransferase TRM13 (1);	0.241155	0.42964	D	0.000633	T	0.42765	0.1217	L	0.54323	1.7	0.80722	D	1	D	0.64830	0.994	P	0.60789	0.879	T	0.40289	-0.9571	10	0.39692	T	0.17	-18.9913	10.4083	0.44278	0.0:0.0726:0.0:0.9274	.	363	Q9NUP7	TRM13_HUMAN	D	363	ENSP00000359160:Y363D	ENSP00000359160:Y363D	Y	+	1	0	CCDC76	100386307	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.470000	0.60175	2.195000	0.70347	0.533000	0.62120	TAT		0.428	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083		34	10	34	10
FTCD	10841	hgsc.bcm.edu;broad.mit.edu	37	21	47574183	47574183	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr21:47574183C>T	ENST00000291670.5	-	2	161	c.118G>A	c.(118-120)Gca>Aca	p.A40T	FTCD_ENST00000397743.1_Missense_Mutation_p.A40T|FTCD_ENST00000359679.2_Missense_Mutation_p.A40T|FTCD_ENST00000397748.1_Missense_Mutation_p.A40T|FTCD_ENST00000355384.2_Missense_Mutation_p.A40T|FTCD_ENST00000397746.3_Missense_Mutation_p.A40T|FTCD_ENST00000498355.2_5'UTR|FTCD-AS1_ENST00000446649.1_RNA	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	40	Formiminotransferase N-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GAAGGGCCTGCGTCCACATCC	0.677																																																0													43.0	40.0	41.0					21																	47574183		2201	4296	6497	SO:0001583	missense	10841			U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.118G>A	21.37:g.47574183C>T	ENSP00000291670:p.Ala40Thr		B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Missense_Mutation	SNP	ENST00000291670.5	37	CCDS13731.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732223	0.30684	.	.	ENSG00000160282	ENST00000291670;ENST00000397748;ENST00000359679;ENST00000355384;ENST00000397746;ENST00000397743	T;T;T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01;-1.01;-1.01	4.33	3.42	0.39159	Formiminotransferas, N- and C-terminal subdomains (1);Formiminotransferase catalytic domain (1);Formiminotransferase, N-terminal subdomain (2);	0.244483	0.40818	N	0.001006	T	0.69242	0.3089	L	0.49256	1.55	0.43029	D	0.994595	B;B;B	0.28208	0.203;0.169;0.072	B;B;B	0.24541	0.054;0.032;0.021	T	0.66598	-0.5883	10	0.56958	D	0.05	.	9.0294	0.36249	0.177:0.6697:0.1532:0.0	.	40;40;40	B7WPK3;O95954-2;O95954	.;.;FTCD_HUMAN	T	40	ENSP00000291670:A40T;ENSP00000380856:A40T;ENSP00000352707:A40T;ENSP00000347545:A40T;ENSP00000380854:A40T;ENSP00000380851:A40T	ENSP00000291670:A40T	A	-	1	0	FTCD	46398611	1.000000	0.71417	0.080000	0.20451	0.053000	0.15095	3.477000	0.53151	0.764000	0.33197	0.478000	0.44815	GCA		0.677	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		3	48	3	48
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			45	54	45	54
PTPN23	25930	hgsc.bcm.edu;broad.mit.edu	37	3	47447437	47447437	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr3:47447437C>A	ENST00000265562.4	+	6	524	c.447C>A	c.(445-447)tgC>tgA	p.C149*	PTPN23_ENST00000431726.1_Nonsense_Mutation_p.C23*	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	149	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATTTCCAGTGCGCAGCCGGCG	0.597																																																0													60.0	53.0	56.0					3																	47447437		2203	4300	6503	SO:0001587	stop_gained	25930			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.447C>A	3.37:g.47447437C>A	ENSP00000265562:p.Cys149*		A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Nonsense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	35	5.486775	0.96323	.	.	ENSG00000076201	ENST00000456221;ENST00000456408;ENST00000265562	.	.	.	5.14	-5.11	0.02901	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3722	14.8953	0.70639	0.0:0.5822:0.0:0.4178	.	.	.	.	X	114;114;149	.	ENSP00000265562:C149X	C	+	3	2	PTPN23	47422441	0.222000	0.23652	0.906000	0.35671	0.883000	0.51084	-0.347000	0.07750	-1.192000	0.02691	-0.302000	0.09304	TGC		0.597	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		4	51	4	51
PIGZ	80235	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	196675277	196675277	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr3:196675277C>A	ENST00000412723.1	-	3	637	c.491G>T	c.(490-492)gGt>gTt	p.G164V	PIGZ_ENST00000443835.1_Intron	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	164					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		GACGTAGGAACCAGACAGCAG	0.617																																																0													110.0	86.0	94.0					3																	196675277		2203	4300	6503	SO:0001583	missense	80235			BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.491G>T	3.37:g.196675277C>A	ENSP00000413405:p.Gly164Val		Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202361	0.58234	.	.	ENSG00000119227	ENST00000412723	T	0.60424	0.19	5.26	4.38	0.52667	.	0.248184	0.28847	N	0.013949	T	0.55784	0.1942	M	0.67397	2.05	0.80722	D	1	B	0.30068	0.267	B	0.34385	0.181	T	0.54543	-0.8278	10	0.35671	T	0.21	-2.27	10.4938	0.44766	0.1507:0.7041:0.1451:0.0	.	164	Q86VD9	PIGZ_HUMAN	V	164	ENSP00000413405:G164V	ENSP00000413405:G164V	G	-	2	0	PIGZ	198159674	0.990000	0.36364	0.537000	0.28052	0.957000	0.61999	3.403000	0.52615	1.369000	0.46134	0.543000	0.68304	GGT		0.617	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		11	33	11	33
FRAS1	80144	hgsc.bcm.edu;broad.mit.edu	37	4	79204003	79204003	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr4:79204003C>A	ENST00000325942.6	+	12	1577	c.1137C>A	c.(1135-1137)tgC>tgA	p.C379*	FRAS1_ENST00000264899.6_Nonsense_Mutation_p.C379*|FRAS1_ENST00000264895.6_Nonsense_Mutation_p.C379*	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	379	VWFC 6. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ATGGCCCTTGCAAGGTGTGTG	0.532																																																0													112.0	116.0	115.0					4																	79204003		2022	4178	6200	SO:0001587	stop_gained	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1137C>A	4.37:g.79204003C>A	ENSP00000326330:p.Cys379*		A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Nonsense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	28.2|28.2|28.2	4.901520|4.901520|4.901520	0.92035|0.92035|0.92035	.|.|.	.|.|.	ENSG00000138759|ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913|ENST00000508900	.|.|.	.|.|.	.|.|.	5.6|5.6|5.6	3.84|3.84|3.84	0.44239|0.44239|0.44239	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|.|T	0.61825|.|0.61825	0.2378|.|0.2378	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|.|T	0.67883|.|0.67883	-0.5555|.|-0.5555	3|.|3	.|0.02654|.	.|T|.	.|1|.	.|.|.	12.7863|12.7863|12.7863	0.57507|0.57507|0.57507	0.0:0.8641:0.0:0.1359|0.0:0.8641:0.0:0.1359|0.0:0.8641:0.0:0.1359	.|.|.	.|.|.	.|.|.	.|.|.	E|X|K	308|379;379;379;119|222	.|.|.	.|ENSP00000264895:C379X|.	A|C|Q	+|+|+	2|3|1	0|2|0	FRAS1|FRAS1|FRAS1	79423027|79423027|79423027	0.972000|0.972000|0.972000	0.33761|0.33761|0.33761	0.998000|0.998000|0.998000	0.56505|0.56505|0.56505	0.691000|0.691000|0.691000	0.40173|0.40173|0.40173	0.544000|0.544000|0.544000	0.23253|0.23253|0.23253	0.682000|0.682000|0.682000	0.31407|0.31407|0.31407	0.563000|0.563000|0.563000	0.77884|0.77884|0.77884	GCA|TGC|CAA		0.532	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			8	132	8	132
NPNT	255743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	106890076	106890076	+	Missense_Mutation	SNP	C	C	A	rs139540458		TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr4:106890076C>A	ENST00000379987.2	+	12	1843	c.1627C>A	c.(1627-1629)Cgt>Agt	p.R543S	NPNT_ENST00000453617.2_Missense_Mutation_p.R560S|NPNT_ENST00000305572.8_Intron|NPNT_ENST00000427316.2_Missense_Mutation_p.R573S|NPNT_ENST00000506666.1_Missense_Mutation_p.R544S|NPNT_ENST00000514622.1_Missense_Mutation_p.R514S	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	543	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		TGAAAAAAGGCGTGGTCACAC	0.448																																																0													151.0	130.0	137.0					4																	106890076		2203	4300	6503	SO:0001583	missense	255743				CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.1627C>A	4.37:g.106890076C>A	ENSP00000369323:p.Arg543Ser		A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999158	0.54147	.	.	ENSG00000168743	ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000506666;ENST00000503451	T;T;T;T;T;T	0.02067	4.47;4.47;4.47;4.47;4.47;4.47	5.52	5.52	0.82312	Concanavalin A-like lectin/glucanase (1);MAM domain (2);	0.486738	0.24415	N	0.038739	T	0.01940	0.0061	N	0.05078	-0.115	0.37293	D	0.90836	B;P;P;P;B	0.48503	0.362;0.82;0.82;0.911;0.182	B;B;B;P;B	0.45881	0.205;0.385;0.298;0.496;0.205	T	0.62120	-0.6921	10	0.87932	D	0	.	9.2751	0.37694	0.2283:0.6352:0.1365:0.0	.	514;544;573;560;543	E9PF04;E9PE64;E9PCQ1;E9PCK8;Q6UXI9	.;.;.;.;NPNT_HUMAN	S	543;560;573;514;544;590	ENSP00000369323:R543S;ENSP00000402884:R560S;ENSP00000389252:R573S;ENSP00000422044:R514S;ENSP00000422474:R544S;ENSP00000426146:R590S	ENSP00000369323:R543S	R	+	1	0	NPNT	107109525	1.000000	0.71417	0.993000	0.49108	0.424000	0.31475	2.023000	0.41040	2.580000	0.87095	0.655000	0.94253	CGT		0.448	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278		16	19	16	19
PPP2CA	5515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	133534841	133534841	+	Missense_Mutation	SNP	A	A	T			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr5:133534841A>T	ENST00000481195.1	-	6	1073	c.793T>A	c.(793-795)Tat>Aat	p.Y265N	CTD-2410N18.5_ENST00000519718.1_Intron	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	265					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|meiotic nuclear division (GO:0007126)|mesoderm development (GO:0007498)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein dephosphorylation (GO:0006470)|protein heterotrimerization (GO:0070208)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of protein autophosphorylation (GO:0031952)|regulation of protein catabolic process (GO:0042176)|regulation of receptor activity (GO:0010469)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	CGATAACAATAGTTTGGAGCA	0.373																																																0													139.0	124.0	129.0					5																	133534841		2203	4300	6503	SO:0001583	missense	5515				CCDS4173.1	5q31.1	2013-01-24	2010-03-05		ENSG00000113575	ENSG00000113575	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9299	protein-coding gene	gene with protein product	"""protein phosphatase 2A catalytic subunit, alpha isoform"""	176915	"""protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform"""			8383590	Standard	NM_002715		Approved	PP2Calpha		P67775	OTTHUMG00000129119	ENST00000481195.1:c.793T>A	5.37:g.133534841A>T	ENSP00000418447:p.Tyr265Asn		P05323|P13197	Missense_Mutation	SNP	ENST00000481195.1	37	CCDS4173.1	.	.	.	.	.	.	.	.	.	.	A	31	5.069954	0.93950	.	.	ENSG00000113575	ENST00000481195	T	0.37235	1.21	5.56	5.56	0.83823	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);	0.000000	0.85682	D	0.000000	T	0.75737	0.3890	H	0.98701	4.305	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.86363	0.1718	10	0.87932	D	0	-8.2192	15.7036	0.77560	1.0:0.0:0.0:0.0	.	265	P67775	PP2AA_HUMAN	N	265	ENSP00000418447:Y265N	ENSP00000418447:Y265N	Y	-	1	0	PPP2CA	133562740	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.950000	0.93019	2.118000	0.64928	0.533000	0.62120	TAT		0.373	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251165.1	NM_002715		16	113	16	113
KIF20A	10112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	137521298	137521298	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr5:137521298G>A	ENST00000394894.3	+	16	2250	c.2024G>A	c.(2023-2025)cGg>cAg	p.R675Q	KIF20A_ENST00000508792.1_Missense_Mutation_p.R657Q	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	675					ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTGGCCCTACGGCGGTCACAA	0.507																																																0													93.0	95.0	95.0					5																	137521298		2203	4300	6503	SO:0001583	missense	10112			AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"""Kinesins"""	9787	protein-coding gene	gene with protein product		605664	"""RAB6 interacting, kinesin-like (rabkinesin6)"""	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.2024G>A	5.37:g.137521298G>A	ENSP00000378356:p.Arg675Gln		B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	37	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185381	0.78677	.	.	ENSG00000112984	ENST00000394894;ENST00000508792	T;T	0.71103	-0.51;-0.54	5.1	5.1	0.69264	.	0.000000	0.40469	N	0.001099	T	0.80369	0.4610	L	0.56769	1.78	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.76575	0.92;0.988	T	0.74188	-0.3746	10	0.13108	T	0.6	-17.3307	18.3012	0.90164	0.0:0.0:1.0:0.0	.	657;675	B4DL79;O95235	.;KI20A_HUMAN	Q	675;657	ENSP00000378356:R675Q;ENSP00000420880:R657Q	ENSP00000378356:R675Q	R	+	2	0	KIF20A	137549197	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	7.147000	0.77382	2.653000	0.90120	0.557000	0.71058	CGG		0.507	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		52	145	52	145
BAG6	7917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31612853	31612853	+	Missense_Mutation	SNP	A	A	C			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr6:31612853A>C	ENST00000375964.6	-	10	1570	c.1257T>G	c.(1255-1257)aaT>aaG	p.N419K	BAG6_ENST00000211379.5_Missense_Mutation_p.N413K|BAG6_ENST00000362049.6_Missense_Mutation_p.N413K|BAG6_ENST00000375976.4_Missense_Mutation_p.N413K|BAG6_ENST00000404765.2_Missense_Mutation_p.N413K|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000439687.2_Missense_Mutation_p.N413K	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	419	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						AGGACTCGACATTGGTAGAAG	0.662																																																0													67.0	83.0	77.0					6																	31612853		1509	2708	4217	SO:0001583	missense	7917			M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1257T>G	6.37:g.31612853A>C	ENSP00000365131:p.Asn419Lys		A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	37	CCDS47403.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.93|13.93	2.382746|2.382746	0.42207|0.42207	.|.	.|.	ENSG00000204463|ENSG00000204463	ENST00000453833|ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771;ENST00000435080	.|T;T;T;T;T;T;T	.|0.46063	.|1.45;1.44;1.45;1.46;0.91;1.48;0.88	4.98|4.98	-0.442|-0.442	0.12253|0.12253	.|.	.|0.431115	.|0.25897	.|N	.|0.027582	T|T	0.03871|0.03871	0.0109|0.0109	N|N	0.08118|0.08118	0|0	0.21579|0.21579	N|N	0.999635|0.999635	.|B;B;B;B;B	.|0.21606	.|0.016;0.039;0.036;0.01;0.058	.|B;B;B;B;B	.|0.18871	.|0.007;0.023;0.013;0.01;0.015	T|T	0.35375|0.35375	-0.9791|-0.9791	5|10	.|0.05959	.|T	.|0.93	.|.	2.2816|2.2816	0.04115|0.04115	0.5717:0.1206:0.177:0.1307|0.5717:0.1206:0.177:0.1307	.|.	.|413;413;413;419;413	.|E7EMZ4;F8VXY4;B0UX85;P46379;P46379-2	.|.;.;.;BAG6_HUMAN;.	G|K	74|413;419;413;413;413;413;413;413	.|ENSP00000365143:N413K;ENSP00000365131:N419K;ENSP00000211379:N413K;ENSP00000384494:N413K;ENSP00000402856:N413K;ENSP00000354875:N413K;ENSP00000397978:N413K	.|ENSP00000211379:N413K	C|N	-|-	1|3	0|2	BAG6|BAG6	31720832|31720832	0.667000|0.667000	0.27484|0.27484	0.995000|0.995000	0.50966|0.50966	0.849000|0.849000	0.48306|0.48306	-0.127000|-0.127000	0.10547|0.10547	0.248000|0.248000	0.21435|0.21435	0.525000|0.525000	0.51046|0.51046	TGT|AAT		0.662	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703		58	76	58	76
DST	667	hgsc.bcm.edu;ucsc.edu	37	6	56483940	56483940	+	Missense_Mutation	SNP	T	T	G			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr6:56483940T>G	ENST00000370765.6	-	23	4999	c.4892A>C	c.(4891-4893)cAc>cCc	p.H1631P	DST_ENST00000361203.3_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	6371					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTTATGCAAGTGTTCATTTGT	0.348																																																0													151.0	152.0	151.0					6																	56483940		2202	4300	6502	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4892A>C	6.37:g.56483940T>G	ENSP00000359801:p.His1631Pro		B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.362451	0.61403	.	.	ENSG00000151914	ENST00000370765	T	0.31769	1.48	5.35	5.35	0.76521	.	.	.	.	.	T	0.13756	0.0333	.	.	.	0.09310	N	0.999998	P	0.41265	0.744	B	0.38327	0.271	T	0.06356	-1.0831	7	0.23891	T	0.37	.	15.6438	0.77033	0.0:0.0:0.0:1.0	.	1631	Q03001-3	.	P	1631	ENSP00000359801:H1631P	ENSP00000359801:H1631P	H	-	2	0	DST	56591899	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	4.754000	0.62191	2.150000	0.67090	0.528000	0.53228	CAC		0.348	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		25	155	25	155
RFX6	222546	hgsc.bcm.edu;broad.mit.edu	37	6	117246787	117246787	+	Missense_Mutation	SNP	T	T	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr6:117246787T>A	ENST00000332958.2	+	16	1866	c.1850T>A	c.(1849-1851)tTc>tAc	p.F617Y		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	617					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CTGCACCAGTTCCCTGCTGGG	0.532																																																0													72.0	64.0	67.0					6																	117246787		2203	4300	6503	SO:0001583	missense	222546			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1850T>A	6.37:g.117246787T>A	ENSP00000332208:p.Phe617Tyr		Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.600777	0.28534	.	.	ENSG00000185002	ENST00000332958	T	0.55052	0.54	5.95	4.78	0.61160	.	0.224709	0.47852	D	0.000213	T	0.22859	0.0552	L	0.39898	1.24	0.42790	D	0.993892	B	0.12630	0.006	B	0.15052	0.012	T	0.09100	-1.0690	10	0.12766	T	0.61	-13.3454	12.122	0.53897	0.0:0.067:0.0:0.933	.	617	Q8HWS3	RFX6_HUMAN	Y	617	ENSP00000332208:F617Y	ENSP00000332208:F617Y	F	+	2	0	RFX6	117353480	1.000000	0.71417	0.836000	0.33094	0.285000	0.27093	4.584000	0.60971	1.068000	0.40764	0.402000	0.26972	TTC		0.532	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		6	67	6	67
SRPK2	6733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	104783594	104783594	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr7:104783594C>T	ENST00000393651.3	-	10	1084	c.997G>A	c.(997-999)Gag>Aag	p.E333K	SRPK2_ENST00000357311.3_Missense_Mutation_p.E322K|SRPK2_ENST00000489828.1_Missense_Mutation_p.E322K	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						AGTTTCACCTCTGGGCAGTAT	0.498																																																0													129.0	118.0	122.0					7																	104783594		2203	4300	6503	SO:0001583	missense	6733			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"""SR protein kinase 2"", ""serine/arginine-rich splicing factor kinase 2"""	602980	"""SFRS protein kinase 2"""			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.997G>A	7.37:g.104783594C>T	ENSP00000377262:p.Glu333Lys			Missense_Mutation	SNP	ENST00000393651.3	37	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001732	0.74932	.	.	ENSG00000135250	ENST00000393651;ENST00000357311;ENST00000489828	T;T;T	0.22743	1.94;1.94;1.94	5.57	5.57	0.84162	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.376195	0.28098	N	0.016602	T	0.19604	0.0471	L	0.38175	1.15	0.58432	D	0.999999	B;B	0.30361	0.277;0.023	B;B	0.30855	0.121;0.019	T	0.05068	-1.0908	10	0.12430	T	0.62	-12.3419	19.5379	0.95262	0.0:1.0:0.0:0.0	.	333;322	P78362-2;P78362	.;SRPK2_HUMAN	K	333;322;322	ENSP00000377262:E333K;ENSP00000349863:E322K;ENSP00000419791:E322K	ENSP00000349863:E322K	E	-	1	0	SRPK2	104570830	0.975000	0.34042	0.964000	0.40570	0.926000	0.56050	2.656000	0.46716	2.623000	0.88846	0.555000	0.69702	GAG		0.498	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		17	99	17	99
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	37730001	37730001	+	Silent	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr8:37730001G>A	ENST00000330843.4	-	4	2331	c.2319C>T	c.(2317-2319)ccC>ccT	p.P773P	RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000522727.1_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	773					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGGGAAGAGGGGGCGCCACTT	0.557																																																0													82.0	86.0	84.0					8																	37730001		2203	4300	6503	SO:0001819	synonymous_variant	80223			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2319C>T	8.37:g.37730001G>A			J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																				0.557	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		30	80	30	80
LIMA1	51474	broad.mit.edu;ucsc.edu	37	12	50598436	50598436	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr12:50598436G>A	ENST00000341247.4	-	6	912	c.763C>T	c.(763-765)Cga>Tga	p.R255*	LIMA1_ENST00000552909.1_Nonsense_Mutation_p.R95*|LIMA1_ENST00000552783.1_Nonsense_Mutation_p.R95*|LIMA1_ENST00000394943.3_Nonsense_Mutation_p.R255*|LIMA1_ENST00000552823.1_Nonsense_Mutation_p.R95*|LIMA1_ENST00000547825.1_5'Flank|LIMA1_ENST00000552008.1_5'UTR	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	255					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TCCAGATTTCGTCTACTCTCA	0.423																																																0													151.0	136.0	141.0					12																	50598436		2203	4300	6503	SO:0001587	stop_gained	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.763C>T	12.37:g.50598436G>A	ENSP00000340184:p.Arg255*		B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Nonsense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475480	0.84640	.	.	ENSG00000050405	ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	.	.	.	5.35	3.21	0.36854	.	0.571421	0.16317	N	0.219738	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1288	0.48334	0.0:0.0:0.5097:0.4903	.	.	.	.	X	95;255;255;95;95;174	.	ENSP00000340184:R255X	R	-	1	2	LIMA1	48884703	0.917000	0.31117	0.953000	0.39169	0.969000	0.65631	1.351000	0.34022	1.365000	0.46057	0.585000	0.79938	CGA		0.423	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		56	71	56	71
OR2G6	391211	broad.mit.edu;ucsc.edu	37	1	248685220	248685220	+	Silent	SNP	C	C	T			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr1:248685220C>T	ENST00000343414.4	+	1	305	c.273C>T	c.(271-273)acC>acT	p.T91T		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T91T(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAGACAAAACCATGAGCTACG	0.517																																																1	Substitution - coding silent(1)	lung(1)											123.0	118.0	119.0					1																	248685220		2203	4300	6503	SO:0001819	synonymous_variant	391211				CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.273C>T	1.37:g.248685220C>T			B2RP33	Silent	SNP	ENST00000343414.4	37	CCDS31119.1																																																																																				0.517	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842		63	94	63	94
TOM1	10043	broad.mit.edu;ucsc.edu	37	22	35726358	35726358	+	Missense_Mutation	SNP	C	C	G			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr22:35726358C>G	ENST00000449058.2	+	8	909	c.784C>G	c.(784-786)Cga>Gga	p.R262G	TOM1_ENST00000411850.1_Missense_Mutation_p.R262G|TOM1_ENST00000425375.1_Missense_Mutation_p.R217G|TOM1_ENST00000436462.2_Missense_Mutation_p.R224G|TOM1_ENST00000447733.1_Missense_Mutation_p.R229G|TOM1_ENST00000382034.5_Missense_Mutation_p.R195G	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	262	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						CCGCACGTGCCGAGCCATGCA	0.537																																																0													126.0	105.0	112.0					22																	35726358		2203	4300	6503	SO:0001583	missense	10043			AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.784C>G	22.37:g.35726358C>G	ENSP00000394466:p.Arg262Gly		B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Missense_Mutation	SNP	ENST00000449058.2	37	CCDS13913.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.083250	0.76642	.	.	ENSG00000100284	ENST00000447733;ENST00000456128;ENST00000449058;ENST00000411850;ENST00000425375;ENST00000451197;ENST00000436462;ENST00000382034	T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.31	4.23	0.50019	GAT (2);	0.103239	0.64402	D	0.000007	T	0.68723	0.3032	M	0.82630	2.6	0.52099	D	0.999944	P;D;D;D;P	0.62365	0.946;0.966;0.991;0.958;0.941	P;P;D;P;P	0.68943	0.671;0.758;0.961;0.551;0.581	T	0.73773	-0.3877	10	0.87932	D	0	-2.2088	13.7111	0.62670	0.2254:0.7746:0.0:0.0	.	217;224;271;262;262	O60784-3;E7EPD0;B4DKQ5;O60784-2;O60784	.;.;.;.;TOM1_HUMAN	G	229;256;262;262;217;271;224;195	ENSP00000398876:R229G;ENSP00000393714:R256G;ENSP00000394466:R262G;ENSP00000413697:R262G;ENSP00000394924:R217G;ENSP00000402556:R224G;ENSP00000371465:R195G	ENSP00000371465:R195G	R	+	1	2	TOM1	34056358	0.998000	0.40836	0.998000	0.56505	0.999000	0.98932	1.951000	0.40333	2.644000	0.89710	0.645000	0.84053	CGA		0.537	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488		96	90	96	90
HEATR1	55127	broad.mit.edu;ucsc.edu	37	1	236738051	236738051	+	Silent	SNP	C	C	T	rs142628625	byFrequency	TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr1:236738051C>T	ENST00000366582.3	-	23	3351	c.3237G>A	c.(3235-3237)ccG>ccA	p.P1079P	HEATR1_ENST00000366581.2_Intron	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1079					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CTAGACTCTTCGGATCCTCAT	0.423													C|||	4	0.000798722	0.003	0.0	5008	,	,		17522	0.0		0.0	False		,,,				2504	0.0															0								C		11,4395	17.9+/-39.9	0,11,2192	65.0	68.0	67.0		3237	-11.7	0.5	1	dbSNP_134	67	0,8596		0,0,4298	no	coding-synonymous	HEATR1	NM_018072.5		0,11,6490	TT,TC,CC		0.0,0.2497,0.0846		1079/2145	236738051	11,12991	2203	4298	6501	SO:0001819	synonymous_variant	55127			BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"""UTP10, small subunit (SSU) processome component, homolog (yeast)"""					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.3237G>A	1.37:g.236738051C>T			Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																				0.423	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		28	43	28	43
NLE1	54475	broad.mit.edu;ucsc.edu	37	17	33464163	33464163	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr17:33464163G>A	ENST00000442241.4	-	7	724	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	NLE1_ENST00000593176.1_5'UTR|NLE1_ENST00000360831.5_Missense_Mutation_p.R187W|NLE1_ENST00000586869.1_5'UTR	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	229					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				TCCCAGATCCGCACACTGCCA	0.617																																																0													62.0	54.0	57.0					17																	33464163		2203	4300	6503	SO:0001583	missense	54475				CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"""WD repeat domain containing"""	19889	protein-coding gene	gene with protein product	"""Notchless gene homolog, (Drosophila)"""						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.685C>T	17.37:g.33464163G>A	ENSP00000413572:p.Arg229Trp		O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848474	0.91277	.	.	ENSG00000073536	ENST00000442241;ENST00000537697	T	0.28454	1.61	4.51	4.51	0.55191	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.56891	0.2016	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.63637	-0.6592	10	0.87932	D	0	-25.4301	14.7766	0.69736	0.0:0.0:1.0:0.0	.	229	Q9NVX2	NLE1_HUMAN	W	229;205	ENSP00000413572:R229W	ENSP00000413572:R229W	R	-	1	2	NLE1	30488276	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.047000	0.76599	2.358000	0.79984	0.591000	0.81541	CGG		0.617	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		18	33	18	33
ARID1A	8289	broad.mit.edu	37	1	27106229	27106230	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-FG-7637-01A-11D-2086-08	TCGA-FG-7637-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aea26718-ba34-444f-9122-0faf73b62ea1	c2346512-f289-4ac1-a8c9-460c4f3f0126	g.chr1:27106229_27106230delAG	ENST00000324856.7	+	20	6211_6212	c.5840_5841delAG	c.(5839-5841)cagfs	p.Q1947fs	ARID1A_ENST00000374152.2_Frame_Shift_Del_p.Q1564fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.Q275fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.Q1730fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1947					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.H1949fs*16(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGCCCAGCACAGAGCCACCGGA	0.53			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Insertion - Frameshift(1)	large_intestine(1)																																								SO:0001589	frameshift_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5840_5841delAG	1.37:g.27106231_27106232delAG	ENSP00000320485:p.Gln1947fs		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																				0.530	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		22	137	22	137
