#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	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_Start_position_hg18	i_TranscriptID	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
CPN1	1369	broad.mit.edu	37	10	101825111	101825111	+	Missense_Mutation	SNP	C	C	T	rs374397752		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr10:101825111C>T	ENST00000370418.3	-	4	844	c.593G>A	c.(592-594)cGg>cAg	p.R198Q		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	198	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R198Q(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		GATCACCGCCCGGGTCTCGGG	0.577																																					p.R198Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G593A	10						.						38.0	38.0	38.0					10																	101825111		2203	4300	6503	101815101	SO:0001583	missense	1369	exon4			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.593G>A	10.37:g.101825111C>T	ENSP00000359446:p.Arg198Gln		101815101	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.618642	0.28801	.	.	ENSG00000120054	ENST00000370418	T	0.12984	2.63	4.62	-4.13	0.03904	Peptidase M14, carboxypeptidase A (2);	1.399120	0.04450	N	0.372338	T	0.08268	0.0206	N	0.17723	0.515	0.18873	N	0.999987	B	0.22211	0.066	B	0.10450	0.005	T	0.35773	-0.9775	10	0.22706	T	0.39	-22.7808	8.5778	0.33609	0.1398:0.5647:0.0:0.2956	.	198	P15169	CBPN_HUMAN	Q	198	ENSP00000359446:R198Q	ENSP00000359446:R198Q	R	-	2	0	CPN1	101815101	0.002000	0.14202	0.013000	0.15412	0.743000	0.42351	0.097000	0.15168	-0.952000	0.03649	-0.367000	0.07326	CGG		0.577	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
MYO3A	53904	broad.mit.edu	37	10	26457646	26457646	+	Silent	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr10:26457646C>T	ENST00000265944.5	+	28	3283	c.3117C>T	c.(3115-3117)ttC>ttT	p.F1039F	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1039	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.F1039F(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TTCAGGTGTTCCTTAAGTATT	0.353																																					p.F1039F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3117T	10						.						92.0	89.0	90.0					10																	26457646		2203	4300	6503	26497652	SO:0001819	synonymous_variant	53904	exon28			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3117C>T	10.37:g.26457646C>T			26497652	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																				0.353	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
MYPN	84665	broad.mit.edu	37	10	69881845	69881845	+	Missense_Mutation	SNP	C	C	T	rs199476403		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr10:69881845C>T	ENST00000358913.5	+	2	1138	c.650C>T	c.(649-651)gCg>gTg	p.A217V	MYPN_ENST00000540630.1_Missense_Mutation_p.A217V|MYPN_ENST00000354393.2_Intron|MYPN_ENST00000373675.3_Missense_Mutation_p.A217V	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	217	Interaction with CARP.		A -> E (in CHM22; dbSNP:rs199476403). {ECO:0000269|PubMed:22286171}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.A217V(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CCTATCCCTGCGGATACCAGG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		20366	0.001		0.0	False		,,,				2504	0.0				p.A217V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C650T	10						.						50.0	48.0	49.0					10																	69881845		2203	4300	6503	69551851	SO:0001583	missense	84665	exon2			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.650C>T	10.37:g.69881845C>T	ENSP00000351790:p.Ala217Val		69551851	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077749	0.36662	.	.	ENSG00000138347	ENST00000358913;ENST00000540630;ENST00000373675	T;T;T	0.61980	0.38;0.36;0.06	5.74	3.76	0.43208	.	1.066890	0.07128	N	0.845013	T	0.39784	0.1091	N	0.14661	0.345	0.09310	N	1	P;B	0.35774	0.519;0.031	B;B	0.24974	0.057;0.01	T	0.09378	-1.0677	9	.	.	.	.	7.8188	0.29276	0.1929:0.6433:0.1638:0.0	.	217;217	Q86TC9-3;Q86TC9	.;MYPN_HUMAN	V	217	ENSP00000351790:A217V;ENSP00000441668:A217V;ENSP00000362779:A217V	.	A	+	2	0	MYPN	69551851	0.316000	0.24580	0.201000	0.23476	0.996000	0.88848	1.523000	0.35932	2.683000	0.91414	0.655000	0.94253	GCG		0.507	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
MTG1	92170	broad.mit.edu	37	10	135233089	135233089	+	Silent	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr10:135233089G>A	ENST00000317502.6	+	10	908	c.858G>A	c.(856-858)acG>acA	p.T286T	MTG1_ENST00000477902.2_Silent_p.T245T|RP11-108K14.8_ENST00000468317.2_Silent_p.T291T	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	286					GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.T286T(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AGGTGCTCACGGGCACGGGTG	0.657																																					p.T286T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G858A	10						.						144.0	97.0	113.0					10																	135233089		2194	4298	6492	135083079	SO:0001819	synonymous_variant	92170	exon10				CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"""GTP-binding protein 7"", ""GTP-binding protein 7 (putative)"", ""mitochondrial GTPase 1 homolog (S. cerevisiae)"""	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	ENST00000317502.6:c.858G>A	10.37:g.135233089G>A			135083079	NM_138384	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Silent	SNP	ENST00000317502.6	37	CCDS31320.1																																																																																				0.657	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384	
ATM	472	broad.mit.edu	37	11	108163375	108163375	+	Missense_Mutation	SNP	G	G	A	rs201594549		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:108163375G>A	ENST00000452508.2	+	31	4655	c.4466G>A	c.(4465-4467)cGt>cAt	p.R1489H	ATM_ENST00000278616.4_Missense_Mutation_p.R1489H			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1489					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R1489H(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GTGTCATTACGTAGCTTCTCC	0.368			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.R1489H		yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4466A	11						.	A	HIS/ARG	0,4402		0,0,2201	258.0	238.0	245.0		4466	4.1	1.0	11		245	1,8595	1.2+/-3.3	0,1,4297	no	missense	ATM	NM_000051.3	29	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1489/3057	108163375	1,12997	2201	4298	6499	107668585	SO:0001583	missense	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4466G>A	11.37:g.108163375G>A	ENSP00000388058:p.Arg1489His		107668585	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	g	24.6	4.554140	0.86231	0.0	1.16E-4	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.70045	-0.45;-0.45	5.01	4.1	0.47936	Armadillo-type fold (1);	0.052007	0.85682	N	0.000000	T	0.76040	0.3932	L	0.56769	1.78	0.39415	D	0.966821	D	0.76494	0.999	D	0.65140	0.932	T	0.77021	-0.2742	10	0.40728	T	0.16	.	13.9441	0.64073	0.0738:0.0:0.9262:0.0	.	1489	Q13315	ATM_HUMAN	H	1489	ENSP00000278616:R1489H;ENSP00000388058:R1489H	ENSP00000278616:R1489H	R	+	2	0	ATM	107668585	1.000000	0.71417	0.968000	0.41197	0.982000	0.71751	5.740000	0.68629	1.237000	0.43756	-0.213000	0.12676	CGT		0.368	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
IGSF9B	22997	broad.mit.edu	37	11	133789652	133789652	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:133789652G>A	ENST00000321016.8	-	18	4198	c.3968C>T	c.(3967-3969)aCg>aTg	p.T1323M	IGSF9B_ENST00000533871.2_Missense_Mutation_p.T1323M			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1323	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.T1323M(1)|p.T779M(1)		breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		AGTAGGTAACGTGGGTGGTGG	0.682																																					p.T1323M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3968T	11						.						12.0	14.0	13.0					11																	133789652		2009	4147	6156	133294862	SO:0001583	missense	22997	exon18			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3968C>T	11.37:g.133789652G>A	ENSP00000317980:p.Thr1323Met		133294862	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	10.51	1.371041	0.24771	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.66280	0.13;-0.2	4.94	4.01	0.46588	.	0.514294	0.16056	N	0.231733	T	0.37919	0.1021	N	0.08118	0	0.09310	N	1	P	0.42337	0.776	B	0.32289	0.143	T	0.22906	-1.0203	10	0.62326	D	0.03	.	12.3966	0.55389	0.0:0.0:0.813:0.187	.	1323	Q9UPX0	TUTLB_HUMAN	M	1323;1165	ENSP00000317980:T1323M;ENSP00000436552:T1165M	ENSP00000317980:T1323M	T	-	2	0	IGSF9B	133294862	1.000000	0.71417	0.009000	0.14445	0.517000	0.34286	4.561000	0.60809	1.231000	0.43661	0.561000	0.74099	ACG		0.682	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
NLRP10	338322	broad.mit.edu	37	11	7981503	7981503	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:7981503C>A	ENST00000328600.2	-	2	1817	c.1656G>T	c.(1654-1656)atG>atT	p.M552I		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	552					defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)	p.M552I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCATAGATTCCATCTGTTCTT	0.388																																					p.M552I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1656T	11						.						62.0	64.0	64.0					11																	7981503		2201	4296	6497	7938079	SO:0001583	missense	338322	exon2			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1656G>T	11.37:g.7981503C>A	ENSP00000327763:p.Met552Ile		7938079	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	C	1.933	-0.445489	0.04604	.	.	ENSG00000182261	ENST00000328600	D	0.87412	-2.25	4.31	-0.966	0.10320	.	0.736942	0.11730	N	0.535024	T	0.66713	0.2817	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.53394	-0.8445	10	0.07030	T	0.85	.	2.9145	0.05748	0.2431:0.3927:0.0:0.3642	.	552	Q86W26	NAL10_HUMAN	I	552	ENSP00000327763:M552I	ENSP00000327763:M552I	M	-	3	0	NLRP10	7938079	0.003000	0.15002	0.000000	0.03702	0.127000	0.20565	0.028000	0.13644	0.056000	0.16144	0.563000	0.77884	ATG		0.388	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
GAS2	2620	broad.mit.edu	37	11	22759270	22759270	+	Silent	SNP	A	A	G			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:22759270A>G	ENST00000454584.2	+	5	734	c.429A>G	c.(427-429)agA>agG	p.R143R	GAS2_ENST00000278187.3_Silent_p.R143R|GAS2_ENST00000433790.1_Silent_p.R143R	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	143	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)		p.R143R(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						AGCAACCCAGAGAAGTGTGTC	0.488																																					p.R143R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A429G	11						.						183.0	158.0	166.0					11																	22759270		2203	4300	6503	22715846	SO:0001819	synonymous_variant	2620	exon5			BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.429A>G	11.37:g.22759270A>G			22715846	NM_001143830	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																				0.488	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553	
OR8K1	390157	broad.mit.edu	37	11	56113768	56113768	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:56113768C>T	ENST00000279783.2	+	1	348	c.254C>T	c.(253-255)cCg>cTg	p.P85L		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P85L(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					GTCATTGCCCCGAAGATGTTA	0.403										HNSCC(65;0.19)																											p.P85L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C254T	11						.						170.0	161.0	164.0					11																	56113768		2201	4296	6497	55870344	SO:0001583	missense	390157	exon1			AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.254C>T	11.37:g.56113768C>T	ENSP00000279783:p.Pro85Leu		55870344	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.722978	0.48728	.	.	ENSG00000150261	ENST00000279783	T	0.01854	4.6	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.130466	0.35151	N	0.003416	T	0.18964	0.0455	H	0.95574	3.69	0.58432	D	0.999999	D	0.76494	0.999	P	0.60949	0.881	T	0.26121	-1.0112	10	0.87932	D	0	-14.31	18.2972	0.90150	0.0:1.0:0.0:0.0	.	85	Q8NGG5	OR8K1_HUMAN	L	85	ENSP00000279783:P85L	ENSP00000279783:P85L	P	+	2	0	OR8K1	55870344	1.000000	0.71417	0.063000	0.19743	0.056000	0.15407	7.354000	0.79424	2.297000	0.77311	0.549000	0.68633	CCG		0.403	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
CATSPER1	117144	broad.mit.edu	37	11	65792739	65792739	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:65792739C>T	ENST00000312106.5	-	1	1249	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	371					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.R371H(1)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						GACACGTGAGCGGATTGTGCT	0.557																																					p.R371H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1112A	11						.						138.0	114.0	122.0					11																	65792739		2201	4296	6497	65549315	SO:0001583	missense	117144	exon1			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1112G>A	11.37:g.65792739C>T	ENSP00000309052:p.Arg371His		65549315	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	0.898	-0.723131	0.03158	.	.	ENSG00000175294	ENST00000312106	D	0.97620	-4.46	2.02	-1.88	0.07713	.	.	.	.	.	D	0.82618	0.5076	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.78738	-0.2087	9	0.10377	T	0.69	0.1168	2.9718	0.05925	0.0:0.3088:0.2419:0.4494	.	371	Q8NEC5	CTSR1_HUMAN	H	371	ENSP00000309052:R371H	ENSP00000309052:R371H	R	-	2	0	CATSPER1	65549315	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.380000	0.00491	-0.509000	0.06532	-2.363000	0.00238	CGC		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
IGSF9B	22997	broad.mit.edu	37	11	133795714	133795714	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr11:133795714G>A	ENST00000321016.8	-	14	2184	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	IGSF9B_ENST00000533871.2_Missense_Mutation_p.R652C			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	652	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.R108C(2)|p.R652C(1)		breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TCTGCGACACGGAACTCCATG	0.592																																					p.R652C												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.C1954T	11						.						53.0	58.0	56.0					11																	133795714		2093	4226	6319	133300924	SO:0001583	missense	22997	exon14			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1954C>T	11.37:g.133795714G>A	ENSP00000317980:p.Arg652Cys		133300924	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	32	5.131897	0.94473	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.59364	0.27;0.27;0.27	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.43747	D	0.000521	T	0.79941	0.4533	M	0.84511	2.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83196	-0.0081	10	0.87932	D	0	.	19.0783	0.93171	0.0:0.0:1.0:0.0	.	652	Q9UPX0	TUTLB_HUMAN	C	652;494;652	ENSP00000317980:R652C;ENSP00000436552:R494C;ENSP00000436576:R652C	ENSP00000317980:R652C	R	-	1	0	IGSF9B	133300924	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	9.748000	0.98867	2.504000	0.84457	0.655000	0.94253	CGT		0.592	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
CHD4	1108	broad.mit.edu	37	12	6701583	6701583	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr12:6701583C>T	ENST00000357008.2	-	19	3087	c.2924G>A	c.(2923-2925)cGt>cAt	p.R975H	CHD4_ENST00000544040.1_Missense_Mutation_p.R968H|CHD4_ENST00000309577.6_Missense_Mutation_p.R975H|CHD4_ENST00000544484.1_Missense_Mutation_p.R972H	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	975					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R975H(10)		central_nervous_system(2)	2						CAGCTCCACACGCACAATTAG	0.517																																					p.R975H	Colon(32;586 792 4568 16848 45314)											.	.	10	Substitution - Missense(10)	endometrium(8)|large_intestine(2)	c.G2924A	12						.						88.0	82.0	84.0					12																	6701583		2203	4300	6503	6571844	SO:0001583	missense	1108	exon19			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2924G>A	12.37:g.6701583C>T	ENSP00000349508:p.Arg975His		6571844	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	33	5.253892	0.95336	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	5.4	5.4	0.78164	SNF2-related (1);	0.000000	0.85682	D	0.000000	T	0.82024	0.4947	L	0.37630	1.12	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.997;1.0;0.994	D	0.83812	0.0242	10	0.87932	D	0	.	19.1812	0.93623	0.0:1.0:0.0:0.0	.	975;975;968	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	H	972;968;975;975;949	ENSP00000440392:R972H;ENSP00000440542:R968H;ENSP00000312419:R975H;ENSP00000349508:R975H	ENSP00000312419:R975H	R	-	2	0	CHD4	6571844	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.743000	0.85020	2.530000	0.85305	0.563000	0.77884	CGT		0.517	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0 	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35T	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
KRT82	3888	broad.mit.edu	37	12	52793858	52793858	+	Missense_Mutation	SNP	C	C	T	rs529536223		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr12:52793858C>T	ENST00000257974.2	-	5	930	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	285	Coil 2.|Rod.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.V285M(1)		endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		ATGCCGTCCACGTCCAGCTCC	0.612													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20645	0.0		0.0	False		,,,				2504	0.0				p.V285M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G853A	12						.						102.0	86.0	92.0					12																	52793858		2203	4300	6503	51080125	SO:0001583	missense	3888	exon5			Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.853G>A	12.37:g.52793858C>T	ENSP00000257974:p.Val285Met		51080125	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	.	.	.	.	.	.	.	.	.	.	C	0.082	-1.181497	0.01633	.	.	ENSG00000161850	ENST00000257974	D	0.88586	-2.4	5.18	1.04	0.20106	Filament (1);	0.532611	0.15770	N	0.245495	T	0.53916	0.1826	N	0.00186	-1.895	0.27603	N	0.948893	B	0.24533	0.105	B	0.21151	0.033	T	0.58393	-0.7644	10	0.10111	T	0.7	.	1.6566	0.02782	0.1103:0.3451:0.2299:0.3147	.	285	Q9NSB4	KRT82_HUMAN	M	285	ENSP00000257974:V285M	ENSP00000257974:V285M	V	-	1	0	KRT82	51080125	0.002000	0.14202	0.002000	0.10522	0.523000	0.34469	-0.851000	0.04313	0.300000	0.22699	0.561000	0.74099	GTG		0.612	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
LRP1	4035	broad.mit.edu	37	12	57570871	57570871	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr12:57570871G>A	ENST00000243077.3	+	25	4505	c.4039G>A	c.(4039-4041)Gag>Aag	p.E1347K		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1347					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.E1347K(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGCCACACCCGAGGGCCTGGC	0.582																																					p.E1347K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4039A	12						.						136.0	117.0	124.0					12																	57570871		2203	4300	6503	55857138	SO:0001583	missense	4035	exon25			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.4039G>A	12.37:g.57570871G>A	ENSP00000243077:p.Glu1347Lys		55857138	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217170	0.79352	.	.	ENSG00000123384	ENST00000243077	D	0.91464	-2.85	5.0	5.0	0.66597	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.91805	0.7407	M	0.92970	3.365	0.80722	D	1	P	0.42375	0.778	B	0.33690	0.168	D	0.93083	0.6493	10	0.46703	T	0.11	.	17.2315	0.86985	0.0:0.0:1.0:0.0	.	1347	Q07954	LRP1_HUMAN	K	1347	ENSP00000243077:E1347K	ENSP00000243077:E1347K	E	+	1	0	LRP1	55857138	1.000000	0.71417	0.977000	0.42913	0.886000	0.51366	9.648000	0.98483	2.602000	0.87976	0.462000	0.41574	GAG		0.582	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
TBX5	6910	broad.mit.edu	37	12	114841666	114841666	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr12:114841666G>A	ENST00000310346.4	-	2	704	c.38C>T	c.(37-39)aCg>aTg	p.T13M	TBX5_ENST00000405440.2_Missense_Mutation_p.T13M|TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000526441.1_Missense_Mutation_p.T13M|TBX5_ENST00000349716.5_Intron	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	13				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.T13M(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CTCCAGAGGCGTGTGCGCCAG	0.687																																					p.T13M	NSCLC(152;1358 1980 4050 23898 40356)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C38T	12						.						27.0	31.0	30.0					12																	114841666		2202	4300	6502	113326049	SO:0001583	missense	6910	exon2			U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.38C>T	12.37:g.114841666G>A	ENSP00000309913:p.Thr13Met		113326049	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184488	0.78677	.	.	ENSG00000089225	ENST00000310346;ENST00000405440;ENST00000526441	D;D;D	0.87887	-2.31;-2.31;-2.28	5.31	5.31	0.75309	.	0.382752	0.28583	N	0.014823	T	0.78805	0.4341	N	0.24115	0.695	0.53005	D	0.999968	P;P	0.47604	0.895;0.898	B;B	0.34138	0.176;0.131	T	0.82589	-0.0382	10	0.56958	D	0.05	.	18.988	0.92780	0.0:0.0:1.0:0.0	.	13;13	Q99593-2;Q99593	.;TBX5_HUMAN	M	13	ENSP00000309913:T13M;ENSP00000384152:T13M;ENSP00000433292:T13M	ENSP00000309913:T13M	T	-	2	0	TBX5	113326049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.381000	0.90152	2.476000	0.83614	0.655000	0.94253	ACG		0.687	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717	
ATP12A	479	broad.mit.edu	37	13	25268673	25268673	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr13:25268673G>A	ENST00000381946.3	+	11	1636	c.1469G>A	c.(1468-1470)cGc>cAc	p.R490H	ATP12A_ENST00000218548.6_Missense_Mutation_p.R496H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	490					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.R490H(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AAAAGAAACCGCAAAGTAGCT	0.393											OREG0022298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R496H	Pancreas(156;1582 1935 18898 22665 26498)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1487A	13						.						120.0	129.0	126.0					13																	25268673		2203	4300	6503	24166673	SO:0001583	missense	479	exon11			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1469G>A	13.37:g.25268673G>A	ENSP00000371372:p.Arg490His	777	24166673	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.049971	0.36181	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.79749	-1.3;-1.3	5.55	-1.36	0.09085	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.667409	0.13957	N	0.351123	T	0.63058	0.2479	N	0.22421	0.69	0.09310	N	0.999993	B;B	0.12013	0.005;0.002	B;B	0.10450	0.005;0.003	T	0.50101	-0.8867	10	0.46703	T	0.11	.	5.3183	0.15868	0.4498:0.2646:0.2855:0.0	.	496;490	P54707-2;P54707	.;AT12A_HUMAN	H	496;490	ENSP00000218548:R496H;ENSP00000371372:R490H	ENSP00000218548:R496H	R	+	2	0	ATP12A	24166673	0.000000	0.05858	0.989000	0.46669	0.995000	0.86356	-0.464000	0.06688	-0.285000	0.09089	0.563000	0.77884	CGC		0.393	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
KCNRG	283518	broad.mit.edu	37	13	50589660	50589660	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr13:50589660G>A	ENST00000312942.1	+	1	271	c.31G>A	c.(31-33)Gtg>Atg	p.V11M	KCNRG_ENST00000360473.4_Missense_Mutation_p.V11M|TRIM13_ENST00000378182.3_3'UTR|TRIM13_ENST00000478111.1_Intron	NM_173605.1	NP_775876.1	Q8N5I3	KCNRG_HUMAN	potassium channel regulator	11	BTB.				protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)	identical protein binding (GO:0042802)	p.V11M(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.48e-10)|COAD - Colon adenocarcinoma(199;0.204)		CACTTTGAATGTGGGAGGGAA	0.423																																					p.V11M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G31A	13						.						144.0	151.0	149.0					13																	50589660		2203	4300	6503	49487661	SO:0001583	missense	283518	exon1				CCDS9424.1, CCDS41889.1	13q14.11	2008-05-02			ENSG00000198553	ENSG00000198553			18893	protein-coding gene	gene with protein product							Standard	NM_173605		Approved		uc001vdu.3	Q8N5I3	OTTHUMG00000140140	ENST00000312942.1:c.31G>A	13.37:g.50589660G>A	ENSP00000324191:p.Val11Met		49487661	NM_199464	A2A2X9|Q0P6D0|Q8IU75|Q8N3Q9	Missense_Mutation	SNP	ENST00000312942.1	37	CCDS9424.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.293048	0.60086	.	.	ENSG00000198553	ENST00000360473;ENST00000312942	T;T	0.66638	-0.22;-0.22	5.6	3.85	0.44370	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.082682	0.50627	D	0.000111	D	0.86058	0.5842	H	0.97707	4.06	0.41997	D	0.990872	P;P	0.50528	0.936;0.879	D;B	0.63113	0.911;0.243	D	0.88440	0.3041	10	0.87932	D	0	.	11.1965	0.48715	0.0691:0.1284:0.8025:0.0	.	11;11	Q8N5I3;Q8N5I3-2	KCNRG_HUMAN;.	M	11	ENSP00000353661:V11M;ENSP00000324191:V11M	ENSP00000324191:V11M	V	+	1	0	KCNRG	49487661	1.000000	0.71417	0.637000	0.29366	0.785000	0.44390	3.241000	0.51376	0.708000	0.31955	0.655000	0.94253	GTG		0.423	KCNRG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276308.1		
KCNRG	283518	broad.mit.edu	37	13	50589805	50589805	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr13:50589805G>T	ENST00000312942.1	+	1	416	c.176G>T	c.(175-177)aGt>aTt	p.S59I	KCNRG_ENST00000360473.4_Missense_Mutation_p.S59I|TRIM13_ENST00000378182.3_3'UTR|TRIM13_ENST00000478111.1_Intron	NM_173605.1	NP_775876.1	Q8N5I3	KCNRG_HUMAN	potassium channel regulator	59	BTB.				protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)	identical protein binding (GO:0042802)	p.S59I(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.48e-10)|COAD - Colon adenocarcinoma(199;0.204)		GATTTGTTTAGTTTCATCTTA	0.398																																					p.S59I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G176T	13						.						163.0	166.0	165.0					13																	50589805		2203	4300	6503	49487806	SO:0001583	missense	283518	exon1				CCDS9424.1, CCDS41889.1	13q14.11	2008-05-02			ENSG00000198553	ENSG00000198553			18893	protein-coding gene	gene with protein product							Standard	NM_173605		Approved		uc001vdu.3	Q8N5I3	OTTHUMG00000140140	ENST00000312942.1:c.176G>T	13.37:g.50589805G>T	ENSP00000324191:p.Ser59Ile		49487806	NM_199464	A2A2X9|Q0P6D0|Q8IU75|Q8N3Q9	Missense_Mutation	SNP	ENST00000312942.1	37	CCDS9424.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316017	0.60524	.	.	ENSG00000198553	ENST00000360473;ENST00000312942	T;T	0.45668	0.89;0.89	5.74	3.97	0.46021	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.113578	0.64402	D	0.000008	T	0.62551	0.2437	M	0.78223	2.4	0.40926	D	0.98435	D;D	0.63046	0.992;0.96	D;P	0.72075	0.976;0.657	T	0.65026	-0.6268	10	0.56958	D	0.05	.	11.3066	0.49338	0.0684:0.1274:0.8042:0.0	.	59;59	Q8N5I3;Q8N5I3-2	KCNRG_HUMAN;.	I	59	ENSP00000353661:S59I;ENSP00000324191:S59I	ENSP00000324191:S59I	S	+	2	0	KCNRG	49487806	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	1.520000	0.35899	0.744000	0.32741	0.655000	0.94253	AGT		0.398	KCNRG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276308.1		
TM9SF1	10548	broad.mit.edu	37	14	24661386	24661386	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr14:24661386G>C	ENST00000261789.4	-	4	1502	c.1144C>G	c.(1144-1146)Ctc>Gtc	p.L382V	TM9SF1_ENST00000524835.1_Missense_Mutation_p.L295V|TM9SF1_ENST00000530611.1_Missense_Mutation_p.L591V|TM9SF1_ENST00000556387.1_Missense_Mutation_p.L591V|TM9SF1_ENST00000396854.4_Missense_Mutation_p.L382V|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000528669.1_Missense_Mutation_p.L382V	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	382					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.L382V(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		CCAGAGAAGAGACTGGTGGTG	0.537																																					p.L382V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1144G	14						.						151.0	151.0	151.0					14																	24661386		2203	4300	6503	23731226	SO:0001583	missense	10548	exon4			U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.1144C>G	14.37:g.24661386G>C	ENSP00000261789:p.Leu382Val		23731226	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812264	0.70912	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000530611	T;T;T;T;D;T	0.82619	0.81;0.81;0.81;0.19;-1.63;0.81	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.90048	0.6892	M	0.80982	2.52	0.58432	D	0.999999	D;P;P	0.55605	0.972;0.89;0.654	P;P;B	0.60415	0.874;0.649;0.377	D	0.90614	0.4554	10	0.56958	D	0.05	-15.8841	16.1986	0.82053	0.0:0.0:1.0:0.0	.	382;382;382	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	V	382;382;591;295;382;591	ENSP00000261789:L382V;ENSP00000432997:L382V;ENSP00000451949:L591V;ENSP00000434387:L295V;ENSP00000380063:L382V;ENSP00000433967:L591V	ENSP00000433967:L591V	L	-	1	0	TM9SF1;RP11-468E2.1	23731226	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.689000	0.91265	2.699000	0.92147	0.655000	0.94253	CTC		0.537	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
PRIMA1	145270	broad.mit.edu	37	14	94187891	94187891	+	Splice_Site	SNP	T	T	G			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr14:94187891T>G	ENST00000393140.1	-	5	463	c.361A>C	c.(361-363)Aaa>Caa	p.K121Q	PRIMA1_ENST00000393143.1_Splice_Site_p.K121Q|PRIMA1_ENST00000316227.3_3'UTR	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	121					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)		p.K121Q(1)		endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		CTCAGTGGTTTCCTGGAAGTG	0.542																																					p.K121Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A361C	14						.						79.0	60.0	66.0					14																	94187891		2203	4300	6503	93257644	SO:0001630	splice_region_variant	145270	exon5				CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"""membrane anchor of acetylcholinesterase"""	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.360-1A>C	14.37:g.94187891T>G			93257644	NM_178013	Q86XR6	Missense_Mutation	SNP	ENST00000393140.1	37	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.440402	0.63067	.	.	ENSG00000175785	ENST00000393140;ENST00000393143	.	.	.	4.65	4.65	0.58169	.	0.311639	0.22581	N	0.058210	T	0.61961	0.2389	L	0.27053	0.805	0.80722	D	1	D	0.61080	0.989	D	0.72625	0.978	T	0.64368	-0.6424	9	0.62326	D	0.03	0.0376	10.4897	0.44744	0.0:0.0:0.0:1.0	.	121	Q86XR5	PRIMA_HUMAN	Q	121	.	ENSP00000376848:K121Q	K	-	1	0	PRIMA1	93257644	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	4.227000	0.58612	1.735000	0.51646	0.482000	0.46254	AAA		0.542	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	Missense_Mutation
AKT1	207	broad.mit.edu	37	14	105240258	105240258	+	Silent	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr14:105240258G>A	ENST00000554581.1	-	7	2173	c.693C>T	c.(691-693)aaC>aaT	p.N231N	AKT1_ENST00000544168.1_Silent_p.N169N|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000402615.2_Silent_p.N231N|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000407796.2_Silent_p.N231N|AKT1_ENST00000554848.1_Silent_p.N231N|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000555528.1_Silent_p.N231N|AKT1_ENST00000349310.3_Silent_p.N231N			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.N231N(1)		NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CCTCGCCCCCGTTGGCGTACT	0.677		1	Mis		"""breast, colorectal, ovarian, NSCLC"""																																p.N231N			Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C693T	14						.						34.0	30.0	32.0					14																	105240258		2203	4299	6502	104311303	SO:0001819	synonymous_variant	207	exon9			M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.693C>T	14.37:g.105240258G>A			104311303	NM_001014432	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																				0.677	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
MYO9A	4649	broad.mit.edu	37	15	72119272	72119272	+	Silent	SNP	C	C	T	rs200173420		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr15:72119272C>T	ENST00000356056.5	-	42	7768	c.7296G>A	c.(7294-7296)tcG>tcA	p.S2432S	MYO9A_ENST00000564571.1_3'UTR|MYO9A_ENST00000424560.1_Silent_p.S2503S|MYO9A_ENST00000444904.1_Silent_p.S2413S	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2432	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.S2432S(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						AAGAGGAGACCGAAGAGTCCA	0.458																																					p.S2432S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G7296A	15						.	T		0,4398		0,0,2199	78.0	79.0	79.0		7296	-8.5	0.0	15		79	3,8591	3.0+/-9.4	0,3,4294	no	coding-synonymous	MYO9A	NM_006901.2		0,3,6493	TT,TC,CC		0.0349,0.0,0.0231		2432/2549	72119272	3,12989	2199	4297	6496	69906326	SO:0001819	synonymous_variant	4649	exon42			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.7296G>A	15.37:g.72119272C>T			69906326	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																				0.458	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
IGF1R	3480	broad.mit.edu	37	15	99459257	99459257	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr15:99459257G>T	ENST00000268035.6	+	9	2504	c.1893G>T	c.(1891-1893)tgG>tgT	p.W631C	IGF1R_ENST00000558762.1_Missense_Mutation_p.W631C	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	631	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.W631C(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TCGTGAAGTGGAACCCTCCCT	0.507																																					p.W631C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1893T	15						.						156.0	149.0	151.0					15																	99459257		2197	4297	6494	97276780	SO:0001583	missense	3480	exon9			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1893G>T	15.37:g.99459257G>T	ENSP00000268035:p.Trp631Cys		97276780	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	G	36	5.954146	0.97139	.	.	ENSG00000140443	ENST00000268035	D	0.92965	-3.14	4.98	4.98	0.66077	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000045	D	0.96731	0.8933	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97371	0.9976	10	0.87932	D	0	.	18.4285	0.90617	0.0:0.0:1.0:0.0	.	631;631	C9J5X1;P08069	.;IGF1R_HUMAN	C	631	ENSP00000268035:W631C	ENSP00000268035:W631C	W	+	3	0	IGF1R	97276780	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.657000	0.98554	2.583000	0.87209	0.591000	0.81541	TGG		0.507	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
LOC81691	81691	broad.mit.edu	37	16	20826321	20826321	+	Silent	SNP	A	A	G			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr16:20826321A>G	ENST00000261377.6	+	4	533	c.324A>G	c.(322-324)ctA>ctG	p.L108L	AC004381.6_ENST00000348433.6_Silent_p.L108L|AC004381.6_ENST00000564274.1_Silent_p.L108L|AC004381.6_ENST00000567297.1_3'UTR|ERI2_ENST00000564349.1_Intron	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2												p.L108L(1)									TGAGTCAGCTACACTTTTACA	0.403																																					p.L108L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A324G	16						.						129.0	118.0	122.0					16																	20826321		2201	4300	6501	20733822	SO:0001819	synonymous_variant	81691	exon4																														ENST00000261377.6:c.324A>G	16.37:g.20826321A>G			20733822	NM_001199053		Silent	SNP	ENST00000261377.6	37	CCDS10591.1																																																																																				0.403	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2		
PYDC1	260434	broad.mit.edu	37	16	31230669	31230669	+	5'Flank	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr16:31230669C>T	ENST00000302964.3	-	0	0				PYDC1_ENST00000568383.1_5'Flank|TRIM72_ENST00000322122.3_Silent_p.F182F	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1						innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)		p.F182F(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						TGCGGGTGTTCCTGGCTGCAC	0.652																																					p.F182F												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C546T	16						.						51.0	55.0	54.0					16																	31230669		2197	4299	6496	31138170	SO:0001631	upstream_gene_variant	493829	exon4				CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"""pyrin domain containing 1"""			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		16.37:g.31230669C>T	Exception_encountered		31138170	NM_001008274	B2R8L4|Q8NFP8	Silent	SNP	ENST00000302964.3	37	CCDS10710.1																																																																																				0.652	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901	
RBFOX1	54715	broad.mit.edu	37	16	7568385	7568385	+	Silent	SNP	C	C	T	rs202136920		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr16:7568385C>T	ENST00000550418.1	+	5	1252	c.264C>T	c.(262-264)acC>acT	p.T88T	RBFOX1_ENST00000436368.2_Silent_p.T108T|RBFOX1_ENST00000311745.5_Silent_p.T108T|RBFOX1_ENST00000422070.4_Silent_p.T131T|RBFOX1_ENST00000547338.1_Silent_p.T88T|RBFOX1_ENST00000552089.1_Silent_p.T124T|RBFOX1_ENST00000553186.1_Silent_p.T88T|RBFOX1_ENST00000340209.4_Silent_p.T93T|RBFOX1_ENST00000355637.4_Silent_p.T108T|RBFOX1_ENST00000547372.1_Silent_p.T131T|RBFOX1_ENST00000535565.2_Silent_p.T124T	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	88					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.T108T(4)|p.T88T(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						TCTCTGGCACCGCCACAGTAA	0.652													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13991	0.0		0.0	False		,,,				2504	0.0				p.T108T	Ovarian(157;934 2567 15163 39509)											.	.	5	Substitution - coding silent(5)	lung(3)|large_intestine(2)	c.C324T	16						.	C	,,,,,	1,4393	2.1+/-5.4	0,1,2196	68.0	67.0	68.0		264,264,264,324,324,324	-0.2	1.0	16		68	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBFOX1	NM_001142333.1,NM_001142334.1,NM_018723.3,NM_145891.2,NM_145892.2,NM_145893.2	,,,,,	0,1,6494	TT,TC,CC		0.0,0.0228,0.0077	,,,,,	88/371,88/398,88/398,108/419,108/393,108/396	7568385	1,12989	2197	4298	6495	7508386	SO:0001819	synonymous_variant	54715	exon2			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.264C>T	16.37:g.7568385C>T			7508386	NM_145893	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	37	CCDS55983.1																																																																																				0.652	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
GRIN2A	2903	broad.mit.edu	37	16	9857910	9857910	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr16:9857910G>A	ENST00000396573.2	-	14	3800	c.3491C>T	c.(3490-3492)aCg>aTg	p.T1164M	GRIN2A_ENST00000535259.1_Missense_Mutation_p.T1007M|GRIN2A_ENST00000396575.2_Missense_Mutation_p.T1164M|GRIN2A_ENST00000330684.3_Missense_Mutation_p.T1164M|GRIN2A_ENST00000404927.2_Missense_Mutation_p.T1164M|GRIN2A_ENST00000562109.1_Missense_Mutation_p.T1164M	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1164					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.T1164M(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CATTGGCAGCGTGGAGTCCCC	0.527																																					p.T1164M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3491T	16						.						124.0	129.0	127.0					16																	9857910		2197	4300	6497	9765411	SO:0001583	missense	2903	exon13				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3491C>T	16.37:g.9857910G>A	ENSP00000379818:p.Thr1164Met		9765411	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	8.850	0.944403	0.18356	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.11385	2.79;2.78;2.78;2.79;2.79	5.31	5.31	0.75309	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.579063	0.20235	N	0.096408	T	0.13243	0.0321	L	0.34521	1.04	0.30440	N	0.776279	P;P;D	0.59357	0.773;0.916;0.985	B;P;P	0.52598	0.322;0.575;0.703	T	0.04115	-1.0976	9	.	.	.	.	7.7658	0.28978	0.1776:0.0:0.8224:0.0	.	1007;1164;1164	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	M	1164;1164;1007;1164;1164	ENSP00000379818:T1164M;ENSP00000385872:T1164M;ENSP00000441572:T1007M;ENSP00000332549:T1164M;ENSP00000379820:T1164M	.	T	-	2	0	GRIN2A	9765411	0.867000	0.29959	0.981000	0.43875	0.339000	0.28857	2.573000	0.46007	2.472000	0.83506	0.650000	0.86243	ACG		0.527	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
CNGB1	1258	broad.mit.edu	37	16	57921801	57921801	+	Silent	SNP	G	G	A	rs371860152		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr16:57921801G>A	ENST00000251102.8	-	32	3480	c.3420C>T	c.(3418-3420)gcC>gcT	p.A1140A	CNGB1_ENST00000564448.1_Silent_p.A1134A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	1140					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.A1140A(1)		breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CCTCCAGCGCGGCCAGTTCTT	0.577																																					p.A1140A	Colon(156;1293 1853 16336 28962 38659)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3420T	16						.						84.0	89.0	87.0					16																	57921801		1897	4110	6007	56479302	SO:0001819	synonymous_variant	1258	exon32			AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.3420C>T	16.37:g.57921801G>A			56479302	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																				0.577	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
MYH8	4626	broad.mit.edu	37	17	10315769	10315769	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr17:10315769C>T	ENST00000403437.2	-	14	1428	c.1334G>A	c.(1333-1335)cGc>cAc	p.R445H	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	445	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.R445H(1)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						CTGGTTGATGCGGGTGACCAT	0.483									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.R445H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1334A	17						.						222.0	208.0	213.0					17																	10315769		2203	4297	6500	10256494	SO:0001583	missense	4626	exon14	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1334G>A	17.37:g.10315769C>T	ENSP00000384330:p.Arg445His		10256494	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	32	5.193020	0.94960	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.88741	-2.42	4.6	4.6	0.57074	Myosin head, motor domain (2);	0.000000	0.42548	U	0.000683	D	0.95481	0.8532	M	0.90759	3.145	0.58432	D	0.99999	D	0.89917	1.0	D	0.83275	0.996	D	0.96458	0.9339	10	0.87932	D	0	.	17.6116	0.88055	0.0:1.0:0.0:0.0	.	445	P13535	MYH8_HUMAN	H	445	ENSP00000384330:R445H	ENSP00000252173:R445H	R	-	2	0	MYH8	10256494	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	7.603000	0.82811	2.391000	0.81399	0.650000	0.86243	CGC		0.483	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
FGF11	2256	broad.mit.edu	37	17	7346427	7346427	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr17:7346427G>C	ENST00000293829.4	+	5	1234	c.640G>C	c.(640-642)Gtc>Ctc	p.V214L	CHRNB1_ENST00000536404.2_5'Flank|RP11-104H15.8_ENST00000576615.1_RNA|FGF11_ENST00000575235.1_Missense_Mutation_p.V90L|FGF11_ENST00000575082.1_Missense_Mutation_p.V90L|FGF11_ENST00000575398.1_Missense_Mutation_p.V90L|FGF11_ENST00000572907.1_Missense_Mutation_p.V90L|CHRNB1_ENST00000576360.1_5'Flank|CHRNB1_ENST00000306071.2_5'Flank|RP11-104H15.10_ENST00000575331.1_RNA|RP11-104H15.7_ENST00000575310.1_RNA	NM_004112.2	NP_004103.1	Q92914	FGF11_HUMAN	fibroblast growth factor 11	214					cell-cell signaling (GO:0007267)|nervous system development (GO:0007399)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	growth factor activity (GO:0008083)	p.V214L(1)		central_nervous_system(1)|large_intestine(3)|ovary(1)|prostate(1)	6		Prostate(122;0.157)				TCTCCACAGTGTCCCCGAGGC	0.612																																					p.V214L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G640C	17						.						106.0	92.0	97.0					17																	7346427		2203	4300	6503	7287151	SO:0001583	missense	2256	exon5				CCDS11105.1	17p13.1	2008-07-18			ENSG00000161958	ENSG00000161958			3667	protein-coding gene	gene with protein product	"""fibroblast growth factor homologous factor 3"""	601514				8790420	Standard	NM_004112		Approved	FHF3, FLJ16061, MGC45269, MGC102953	uc002ggz.3	Q92914	OTTHUMG00000108136	ENST00000293829.4:c.640G>C	17.37:g.7346427G>C	ENSP00000293829:p.Val214Leu		7287151	NM_004112	Q2YDX8	Missense_Mutation	SNP	ENST00000293829.4	37	CCDS11105.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.049327	0.36181	.	.	ENSG00000161958	ENST00000293829	T	0.65364	-0.15	4.96	4.96	0.65561	.	0.066496	0.64402	D	0.000014	T	0.56062	0.1960	N	0.05031	-0.125	0.49798	D	0.999829	P;D	0.58970	0.643;0.984	B;D	0.65443	0.417;0.935	T	0.51076	-0.8751	10	0.08381	T	0.77	.	16.0624	0.80847	0.0:0.0:1.0:0.0	.	155;214	B7Z1C3;Q92914	.;FGF11_HUMAN	L	214	ENSP00000293829:V214L	ENSP00000293829:V214L	V	+	1	0	FGF11	7287151	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.148000	0.50647	2.734000	0.93682	0.591000	0.81541	GTC		0.612	FGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226939.3	NM_004112	
KRTAP1-3	81850	broad.mit.edu	37	17	39190779	39190779	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr17:39190779T>C	ENST00000344363.5	-	1	328	c.295A>G	c.(295-297)Agt>Ggt	p.S99G		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	109						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.S99G(2)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ACAGCTCCACTGCTGCCCTCC	0.652																																					p.S99G												.	.	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.A295G	17						.						17.0	22.0	21.0					17																	39190779		2007	4147	6154	36444305	SO:0001583	missense	81850	exon1			AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.295A>G	17.37:g.39190779T>C	ENSP00000344420:p.Ser99Gly		36444305	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	T	12.64	1.997470	0.35226	.	.	ENSG00000221880	ENST00000344363	T	0.38077	1.16	4.93	-9.87	0.00470	.	.	.	.	.	T	0.25754	0.0627	.	.	.	0.09310	N	0.999999	B	0.29253	0.239	B	0.34038	0.174	T	0.43956	-0.9359	8	0.59425	D	0.04	.	10.9204	0.47161	0.1862:0.0:0.0722:0.7416	.	109	Q8IUG1	KRA13_HUMAN	G	99	ENSP00000344420:S99G	ENSP00000344420:S99G	S	-	1	0	KRTAP1-3	36444305	0.028000	0.19301	0.006000	0.13384	0.225000	0.24961	0.193000	0.17116	-1.956000	0.01022	-0.302000	0.09304	AGT		0.652	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1		
SMAD4	4089	broad.mit.edu	37	18	48604706	48604706	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr18:48604706G>A	ENST00000342988.3	+	12	2066	c.1528G>A	c.(1528-1530)Gga>Aga	p.G510R	SMAD4_ENST00000588745.1_Missense_Mutation_p.G414R|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.G510R	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	510	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.G510R(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GAAAGGCTGGGGACCGGATTA	0.468																																					p.G510R												.	.	39	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)	pancreas(26)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.G1528A	18						.						112.0	102.0	105.0					18																	48604706		2203	4300	6503	46858704	SO:0001583	missense	4089	exon12			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1528G>A	18.37:g.48604706G>A	ENSP00000341551:p.Gly510Arg		46858704	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316734	0.81469	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.99814	-6.89;-6.89	6.08	6.08	0.98989	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.097482	0.64402	D	0.000001	D	0.99864	0.9936	H	0.95712	3.71	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.97081	0.9784	10	0.87932	D	0	.	19.4362	0.94796	0.0:0.0:1.0:0.0	.	510	Q13485	SMAD4_HUMAN	R	510	ENSP00000341551:G510R;ENSP00000381452:G510R	ENSP00000341551:G510R	G	+	1	0	SMAD4	46858704	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.586000	0.98226	2.890000	0.99128	0.655000	0.94253	GGA		0.468	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
NFATC1	4772	broad.mit.edu	37	18	77170871	77170871	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr18:77170871delC	ENST00000427363.2	+	2	596	c.596delC	c.(595-597)tccfs	p.S199fs	NFATC1_ENST00000592223.1_Frame_Shift_Del_p.S186fs|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000253506.5_Frame_Shift_Del_p.S199fs|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000318065.5_Frame_Shift_Del_p.S186fs|NFATC1_ENST00000329101.4_Frame_Shift_Del_p.S186fs|NFATC1_ENST00000586434.1_Frame_Shift_Del_p.S186fs|NFATC1_ENST00000587635.1_Frame_Shift_Del_p.S199fs|NFATC1_ENST00000542384.1_Frame_Shift_Del_p.S199fs|NFATC1_ENST00000591814.1_Frame_Shift_Del_p.S199fs			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	199	Trans-activation domain A (TAD-A).				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CCGTACGCGTCCCCCCAGACG	0.682																																					p.S199fs	GBM(151;1210 2593 28719 45011)											.	.	0			c.596delC	18						.						67.0	71.0	69.0					18																	77170871		2203	4299	6502	75271859	SO:0001589	frameshift_variant	4772	exon2			U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.596delC	18.37:g.77170871delC	ENSP00000389377:p.Ser199fs		75271859	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Frame_Shift_Del	DEL	ENST00000427363.2	37																																																																																					0.682	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
CRLF1	9244	broad.mit.edu	37	19	18704893	18704893	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr19:18704893T>C	ENST00000392386.3	-	8	1430	c.1237A>G	c.(1237-1239)Aga>Gga	p.R413G	CRLF1_ENST00000594325.1_Intron	NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	413					negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.R413G(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						GTGCCCCGTCTGCCCGAGGGC	0.682																																					p.R413G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1237G	19						.						12.0	11.0	11.0					19																	18704893		2166	4261	6427	18565893	SO:0001583	missense	9244	exon8			AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"""Fibronectin type III domain containing"""	2364	protein-coding gene	gene with protein product	"""cold-induced sweating syndrome"""	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.1237A>G	19.37:g.18704893T>C	ENSP00000376188:p.Arg413Gly		18565893	NM_004750	Q9UHH5	Missense_Mutation	SNP	ENST00000392386.3	37	CCDS32962.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.288800	0.40494	.	.	ENSG00000006016	ENST00000392386	D	0.82344	-1.6	4.21	1.94	0.25998	.	0.155246	0.29940	N	0.010808	T	0.76877	0.4049	N	0.08118	0	0.30009	N	0.815338	D	0.54601	0.967	P	0.60789	0.879	T	0.73322	-0.4019	10	0.87932	D	0	-6.9063	7.9612	0.30072	0.0:0.0:0.4161:0.5839	.	413	O75462	CRLF1_HUMAN	G	413	ENSP00000376188:R413G	ENSP00000376188:R413G	R	-	1	2	CRLF1	18565893	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	0.921000	0.28718	0.141000	0.18875	0.260000	0.18958	AGA		0.682	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1		
NANOS2	339345	broad.mit.edu	37	19	46417701	46417701	+	Missense_Mutation	SNP	G	G	A	rs377721853		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr19:46417701G>A	ENST00000341294.2	-	1	335	c.251C>T	c.(250-252)cCg>cTg	p.P84L		NM_001029861.2	NP_001025032.1	P60321	NANO2_HUMAN	nanos homolog 2 (Drosophila)	84					germ-line stem cell maintenance (GO:0030718)|mRNA catabolic process (GO:0006402)|multicellular organismal development (GO:0007275)|negative regulation of meiosis (GO:0045835)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	mRNA binding (GO:0003729)|zinc ion binding (GO:0008270)	p.P84L(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	6		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		CACGCCATCCGGTGTCTTCAG	0.657																																					p.P84L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C251T	19						.						70.0	63.0	65.0					19																	46417701		2203	4300	6503	51109541	SO:0001583	missense	339345	exon1			BC042883	CCDS33056.1	19q13.32	2003-12-01				ENSG00000188425			23292	protein-coding gene	gene with protein product		608228				12947200, 12690449	Standard	NM_001029861		Approved	NOS2	uc002pdu.3	P60321		ENST00000341294.2:c.251C>T	19.37:g.46417701G>A	ENSP00000341021:p.Pro84Leu		51109541	NM_001029861	Q17R30|Q4G0P8	Missense_Mutation	SNP	ENST00000341294.2	37	CCDS33056.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.776269	0.31411	.	.	ENSG00000188425	ENST00000341294	T	0.40756	1.02	4.65	3.59	0.41128	Zinc finger, nanos-type (2);	0.277593	0.28521	N	0.015047	T	0.26159	0.0638	N	0.17345	0.48	0.09310	N	1	D	0.60575	0.988	P	0.44447	0.45	T	0.06162	-1.0842	10	0.34782	T	0.22	-2.7231	7.6457	0.28318	0.0:0.1821:0.6297:0.1882	.	84	P60321	NANO2_HUMAN	L	84	ENSP00000341021:P84L	ENSP00000341021:P84L	P	-	2	0	NANOS2	51109541	0.007000	0.16637	0.009000	0.14445	0.280000	0.26924	1.490000	0.35573	1.152000	0.42452	0.491000	0.48974	CCG		0.657	NANOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461685.1		
TSKS	60385	broad.mit.edu	37	19	50251423	50251423	+	Silent	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr19:50251423G>A	ENST00000246801.3	-	4	580	c.498C>T	c.(496-498)agC>agT	p.S166S	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	166					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.S166S(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CAGAACACTCGCTCTGGAGCA	0.557																																					p.S166S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C498T	19						.						121.0	102.0	108.0					19																	50251423		2203	4300	6503	54943235	SO:0001819	synonymous_variant	60385	exon4			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.498C>T	19.37:g.50251423G>A			54943235	NM_021733	Q8WXJ0	Silent	SNP	ENST00000246801.3	37	CCDS12780.1																																																																																				0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
SHANK1	50944	broad.mit.edu	37	19	51165688	51165688	+	Missense_Mutation	SNP	G	G	A	rs374977074		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr19:51165688G>A	ENST00000293441.1	-	23	6038	c.6020C>T	c.(6019-6021)tCg>tTg	p.S2007L	SHANK1_ENST00000391813.1_Missense_Mutation_p.S1394L|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000359082.3_Missense_Mutation_p.S1998L|SHANK1_ENST00000391814.1_Missense_Mutation_p.S2015L|SHANK1_ENST00000483981.2_5'UTR	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2007					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)	p.S2007L(1)		breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CTTGTGCTCCGAGGCGGGCAG	0.711																																					p.S2007L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6020T	19						.	G	LEU/SER	0,4324		0,0,2162	12.0	12.0	12.0		6020	3.6	1.0	19		12	2,8486		0,2,4242	no	missense	SHANK1	NM_016148.2	145	0,2,6404	AA,AG,GG		0.0236,0.0,0.0156	probably-damaging	2007/2162	51165688	2,12810	2162	4244	6406	55857500	SO:0001583	missense	50944	exon23			AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.6020C>T	19.37:g.51165688G>A	ENSP00000293441:p.Ser2007Leu		55857500	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	g	10.20	1.285886	0.23478	0.0	2.36E-4	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.39787	1.16;1.64;1.17;1.06	3.64	3.64	0.41730	.	1.526400	0.04832	U	0.438989	T	0.57888	0.2084	L	0.46157	1.445	0.27905	N	0.938828	D;D	0.69078	0.994;0.997	P;D	0.66847	0.885;0.947	T	0.45731	-0.9241	10	0.38643	T	0.18	.	11.0167	0.47693	0.0:0.0:1.0:0.0	.	2007;1394	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	L	2007;1394;1998;2015	ENSP00000293441:S2007L;ENSP00000375689:S1394L;ENSP00000351984:S1998L;ENSP00000375690:S2015L	ENSP00000293441:S2007L	S	-	2	0	SHANK1	55857500	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	2.703000	0.47110	2.045000	0.60652	0.455000	0.32223	TCG		0.711	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148	
AHCYL1	10768	broad.mit.edu	37	1	110555016	110555016	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:110555016G>A	ENST00000369799.5	+	4	776	c.409G>A	c.(409-411)Gct>Act	p.A137T	AHCYL1_ENST00000359172.3_Missense_Mutation_p.A90T|AHCYL1_ENST00000393614.4_Missense_Mutation_p.A90T|AHCYL1_ENST00000475081.1_3'UTR	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	137					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)	p.A137T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		CAGGAAACGTGCTCAGGGGGA	0.512																																					p.A137T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G409A	1						.						85.0	88.0	87.0					1																	110555016		2203	4300	6503	110356539	SO:0001583	missense	10768	exon4			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"""inositol 1,4,5-trisphosphate receptor-binding protein"", ""protein phosphatase 1, regulatory subunit 78"""	607826	"""S-adenosylhomocysteine hydrolase-like 1"""			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.409G>A	1.37:g.110555016G>A	ENSP00000358814:p.Ala137Thr		110356539	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070615	0.76301	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	T;T;T	0.76968	-1.06;-1.06;-1.06	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.76751	0.4031	M	0.84082	2.675	0.80722	D	1	P	0.42735	0.788	B	0.39068	0.289	T	0.82010	-0.0669	10	0.66056	D	0.02	-14.7255	19.8772	0.96880	0.0:0.0:1.0:0.0	.	137	O43865	SAHH2_HUMAN	T	137;90;90	ENSP00000358814:A137T;ENSP00000352092:A90T;ENSP00000377238:A90T	ENSP00000352092:A90T	A	+	1	0	AHCYL1	110356539	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.686000	0.91538	0.650000	0.86243	GCT		0.512	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1		
ADORA3	140	broad.mit.edu	37	1	112043140	112043140	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:112043140G>C	ENST00000241356.4	-	2	794	c.389C>G	c.(388-390)gCc>gGc	p.A130G	ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000486342.1_5'UTR	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	130					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AAGGCCCAGGGCCAGCCATAT	0.507																																					p.A130G												.	.	0			c.C389G	1						.						86.0	96.0	93.0					1																	112043140		2203	4300	6503	111844663	SO:0001583	missense	140	exon2			BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.389C>G	1.37:g.112043140G>C	ENSP00000241356:p.Ala130Gly		111844663	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.649748	0.47362	.	.	ENSG00000121933	ENST00000241356	T	0.38401	1.14	5.35	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.22627	0.0546	M	0.78223	2.4	0.30504	N	0.770107	B	0.11235	0.004	B	0.08055	0.003	T	0.22487	-1.0215	9	0.87932	D	0	.	10.2735	0.43497	0.0758:0.1367:0.7875:0.0	.	130	P33765	AA3R_HUMAN	G	130	ENSP00000241356:A130G	ENSP00000241356:A130G	A	-	2	0	ADORA3	111844663	1.000000	0.71417	0.986000	0.45419	0.991000	0.79684	4.162000	0.58177	0.721000	0.32231	-0.150000	0.13652	GCC		0.507	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
HRNR	388697	broad.mit.edu	37	1	152187551	152187551	+	Missense_Mutation	SNP	C	C	T	rs200451128		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:152187551C>T	ENST00000368801.2	-	3	6629	c.6554G>A	c.(6553-6555)cGc>cAc	p.R2185H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2185					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R2185H(2)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTCGGCCGCGGCTAGGGGA	0.647																																					p.R2185H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G6554A	1						.						21.0	25.0	24.0					1																	152187551		2166	4278	6444	150454175	SO:0001583	missense	388697	exon3			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6554G>A	1.37:g.152187551C>T	ENSP00000357791:p.Arg2185His		150454175	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.811	0.334004	0.11013	.	.	ENSG00000197915	ENST00000368801	T	0.01599	4.74	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00300	0.0009	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.48080	-0.9066	9	0.14252	T	0.57	.	1.9709	0.03406	0.1978:0.2038:0.3952:0.2031	.	2185	Q86YZ3	HORN_HUMAN	H	2185	ENSP00000357791:R2185H	ENSP00000357791:R2185H	R	-	2	0	HRNR	150454175	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.876000	0.00051	-2.560000	0.00474	-0.132000	0.14878	CGC		0.647	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
MST1L	11223	broad.mit.edu	37	1	17084730	17084730	+	RNA	DEL	G	G	-	rs369371609		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:17084730delG	ENST00000455405.2	-	0	286							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.R494fs*37(1)									AAGCACTGCCGGGCAGTCAGT	0.582																																					.												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	.	1						.																																			16957317			11223	.			U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084730delG			16957317	.	B7WPB1|Q13209	Frame_Shift_Del	DEL	ENST00000455405.2	37																																																																																					0.582	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
NFIA	4774	broad.mit.edu	37	1	61553863	61553863	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:61553863C>T	ENST00000403491.3	+	2	554	c.70C>T	c.(70-72)Cga>Tga	p.R24*	NFIA_ENST00000371187.3_Nonsense_Mutation_p.R24*|NFIA_ENST00000485903.2_Nonsense_Mutation_p.R24*|NFIA_ENST00000371184.2_Nonsense_Mutation_p.R24*|NFIA_ENST00000479364.1_Intron|NFIA_ENST00000371185.2_Nonsense_Mutation_p.R24*|NFIA_ENST00000407417.3_Nonsense_Mutation_p.R16*|NFIA_ENST00000371191.1_Nonsense_Mutation_p.R47*|NFIA_ENST00000371189.4_Nonsense_Mutation_p.R69*	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	24					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R24*(1)	NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						GCCCCACGTCCGAGCCTTTGC	0.383																																					p.R69X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C205T	1						.						101.0	110.0	107.0					1																	61553863		2203	4300	6503	61326451	SO:0001587	stop_gained	4774	exon3			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.70C>T	1.37:g.61553863C>T	ENSP00000384523:p.Arg24*		61326451	NM_001145512	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Nonsense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	C	41	8.701549	0.98920	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371185;ENST00000371184;ENST00000371187	.	.	.	5.86	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1267	16.5552	0.84483	0.1316:0.8684:0.0:0.0	.	.	.	.	X	47;16;69;24;24;24;24;24	.	ENSP00000360226:R24X	R	+	1	2	NFIA	61326451	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.910000	0.69931	1.580000	0.49851	0.650000	0.86243	CGA		0.383	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595	
XPR1	9213	broad.mit.edu	37	1	180775220	180775220	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr1:180775220G>A	ENST00000367590.4	+	5	668	c.470G>A	c.(469-471)cGa>cAa	p.R157Q	XPR1_ENST00000367589.3_Missense_Mutation_p.R157Q	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	157	SPX. {ECO:0000255|PROSITE- ProRule:PRU00714}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.R157Q(2)|p.R157L(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						ACAGGGTTTCGAAAAATCCTG	0.378																																					p.R157Q												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.G470A	1						.						52.0	54.0	53.0					1																	180775220		2203	4300	6503	179041843	SO:0001583	missense	9213	exon5			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.470G>A	1.37:g.180775220G>A	ENSP00000356562:p.Arg157Gln		179041843	NM_001135669	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.047138	0.93740	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.51574	0.7	5.42	4.5	0.54988	SPX, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.70103	-0.4964	10	0.87932	D	0	-5.5262	13.8971	0.63778	0.0745:0.0:0.9255:0.0	.	157;157	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	Q	157	ENSP00000356562:R157Q	ENSP00000356561:R157Q	R	+	2	0	XPR1	179041843	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.338000	0.96553	1.294000	0.44707	0.484000	0.47621	CGA		0.378	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
CCM2L	140706	broad.mit.edu	37	20	30605679	30605679	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr20:30605679C>A	ENST00000300415.8	+	3	288	c.275C>A	c.(274-276)aCc>aAc	p.T92N	CCM2L_ENST00000262659.8_Missense_Mutation_p.T92N			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	92								p.T92N(1)									CTGCTAGACACCGCCAGGGTG	0.627																																					p.T92N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C275A	20						.						109.0	109.0	109.0					20																	30605679		2203	4300	6503	30069340	SO:0001583	missense	140706	exon3			AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 160"""	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.275C>A	20.37:g.30605679C>A	ENSP00000300415:p.Thr92Asn		30069340	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	37		.	.	.	.	.	.	.	.	.	.	C	13.54	2.268061	0.40095	.	.	ENSG00000101331	ENST00000300415;ENST00000339619;ENST00000262659	T;T	0.53857	0.6;0.6	4.27	3.29	0.37713	.	0.000000	0.85682	D	0.000000	T	0.45115	0.1326	L	0.32530	0.975	0.46260	D	0.998957	P	0.44478	0.836	P	0.46758	0.526	T	0.19778	-1.0295	10	0.15952	T	0.53	-18.8033	12.6524	0.56768	0.1667:0.8333:0.0:0.0	.	92	Q9NUG4-2	.	N	92	ENSP00000300415:T92N;ENSP00000262659:T92N	ENSP00000262659:T92N	T	+	2	0	C20orf160	30069340	0.999000	0.42202	0.852000	0.33557	0.944000	0.59088	4.115000	0.57865	1.081000	0.41110	0.462000	0.41574	ACC		0.627	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625	
PTPRT	11122	broad.mit.edu	37	20	41400169	41400169	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr20:41400169C>T	ENST00000373187.1	-	5	589	c.590G>A	c.(589-591)cGa>cAa	p.R197Q	PTPRT_ENST00000373193.3_Missense_Mutation_p.R197Q|PTPRT_ENST00000373190.1_Missense_Mutation_p.R197Q|PTPRT_ENST00000356100.2_Missense_Mutation_p.R197Q|PTPRT_ENST00000373184.1_Missense_Mutation_p.R197Q|PTPRT_ENST00000373201.1_Missense_Mutation_p.R197Q|PTPRT_ENST00000373198.4_Missense_Mutation_p.R197Q			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	197	Ig-like C2-type.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.R197Q(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GTTTTGGAGTCGCAGAAAATG	0.498																																					p.R197Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G590A	20						.						142.0	129.0	134.0					20																	41400169		1959	4162	6121	40833583	SO:0001583	missense	11122	exon5			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.590G>A	20.37:g.41400169C>T	ENSP00000362283:p.Arg197Gln		40833583	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613674	0.87359	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.35789	1.3;1.29;1.29;1.29;1.29;1.3;1.3	5.45	5.45	0.79879	Immunoglobulin-like (1);	0.070857	0.64402	D	0.000019	T	0.48519	0.1504	L	0.60455	1.87	0.80722	D	1	D;D	0.64830	0.994;0.99	P;B	0.49922	0.626;0.422	T	0.51276	-0.8726	10	0.87932	D	0	.	19.6268	0.95680	0.0:1.0:0.0:0.0	.	197;197	O14522-1;O14522	.;PTPRT_HUMAN	Q	197	ENSP00000362286:R197Q;ENSP00000362283:R197Q;ENSP00000362289:R197Q;ENSP00000348408:R197Q;ENSP00000362294:R197Q;ENSP00000362280:R197Q;ENSP00000362297:R197Q	ENSP00000348408:R197Q	R	-	2	0	PTPRT	40833583	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.385000	0.79763	2.711000	0.92665	0.650000	0.86243	CGA		0.498	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
KCNG1	3755	broad.mit.edu	37	20	49626415	49626415	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr20:49626415C>T	ENST00000371571.4	-	2	746	c.461G>A	c.(460-462)tGg>tAg	p.W154*	RP5-955M13.4_ENST00000424566.1_RNA|KCNG1_ENST00000506387.1_5'Flank|KCNG1_ENST00000396017.3_Nonsense_Mutation_p.W154*	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	154					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)	p.W154*(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CGCGATGCCCCAGTACAGCAG	0.667																																					p.W154X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G461A	20						.						39.0	39.0	39.0					20																	49626415		2203	4298	6501	49059822	SO:0001587	stop_gained	3755	exon2			AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.461G>A	20.37:g.49626415C>T	ENSP00000360626:p.Trp154*		49059822	NM_002237	A8K3S4|O43528|Q5JXL5|Q9BRC1	Nonsense_Mutation	SNP	ENST00000371571.4	37	CCDS13436.1	.	.	.	.	.	.	.	.	.	.	C	39	7.685497	0.98431	.	.	ENSG00000026559	ENST00000371571;ENST00000396017;ENST00000439216;ENST00000424171	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7261	0.96164	0.0:1.0:0.0:0.0	.	.	.	.	X	154	.	.	W	-	2	0	KCNG1	49059822	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.667000	0.90743	0.561000	0.74099	TGG		0.667	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237	
BRWD1	54014	broad.mit.edu	37	21	40582780	40582780	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr21:40582780C>T	ENST00000333229.2	-	35	4303	c.3976G>A	c.(3976-3978)Gtg>Atg	p.V1326M	BRWD1_ENST00000380800.3_Missense_Mutation_p.V1326M|BRWD1_ENST00000342449.3_Missense_Mutation_p.V1326M	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1326					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V1326M(2)		cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				ATTAAGTTCACTAGTTCCTTA	0.353																																					p.V1326M	Melanoma(170;988 1986 4794 16843 39731)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3976A	21						.						124.0	113.0	117.0					21																	40582780		2203	4300	6503	39504650	SO:0001583	missense	54014	exon35			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3976G>A	21.37:g.40582780C>T	ENSP00000330753:p.Val1326Met		39504650	NM_033656	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357648	0.61293	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.27890	1.64;1.64;1.64	5.34	3.46	0.39613	Bromodomain (4);	0.302742	0.27311	N	0.019948	T	0.21550	0.0519	L	0.41961	1.31	0.80722	D	1	B;P	0.38110	0.178;0.618	B;B	0.31614	0.063;0.133	T	0.05194	-1.0900	10	0.56958	D	0.05	-2.1873	8.0276	0.30446	0.0:0.7173:0.1437:0.139	.	1326;1326	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	M	1326	ENSP00000330753:V1326M;ENSP00000344333:V1326M;ENSP00000370178:V1326M	ENSP00000330753:V1326M	V	-	1	0	BRWD1	39504650	0.834000	0.29399	1.000000	0.80357	0.998000	0.95712	0.894000	0.28350	1.338000	0.45544	0.573000	0.79308	GTG		0.353	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
TRABD	80305	broad.mit.edu	37	22	50636297	50636299	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	GAT	GAT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr22:50636297_50636299delGAT	ENST00000303434.4	+	8	836_838	c.717_719delGAT	c.(715-720)cagatg>cag	p.M241del	TRABD_ENST00000395827.1_In_Frame_Del_p.M241del|TRABD_ENST00000380909.4_In_Frame_Del_p.M241del|TRABD_ENST00000395829.1_In_Frame_Del_p.M241del|RP3-402G11.26_ENST00000608025.1_RNA	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	241								p.M241delM(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		TACTGGAGCAGATGATGGCCGAG	0.65																																					p.239_240del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.717_719del	22						.																																			48978426	SO:0001651	inframe_deletion	80305	exon8			AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.717_719delGAT	22.37:g.50636300_50636302delGAT	ENSP00000305664:p.Met241del		48978424	NM_025204	Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	In_Frame_Del	DEL	ENST00000303434.4	37	CCDS14086.1																																																																																				0.650	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204	
TPO	7173	broad.mit.edu	37	2	1507809	1507809	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:1507809G>A	ENST00000345913.4	+	14	2567	c.2476G>A	c.(2476-2478)Gcg>Acg	p.A826T	TPO_ENST00000382198.1_Missense_Mutation_p.A653T|TPO_ENST00000337415.3_Missense_Mutation_p.A826T|TPO_ENST00000349624.3_Missense_Mutation_p.A653T|TPO_ENST00000346956.3_Intron|TPO_ENST00000329066.4_Missense_Mutation_p.A826T|TPO_ENST00000382201.3_Missense_Mutation_p.A769T|TPO_ENST00000497517.2_3'UTR	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	826	EGF-like; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.A826T(2)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GTGTCTCTGCGCGGACCCCTA	0.577																																					p.A769T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2305A	2						.						84.0	80.0	81.0					2																	1507809		2203	4300	6503	1486816	SO:0001583	missense	7173	exon13				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2476G>A	2.37:g.1507809G>A	ENSP00000318820:p.Ala826Thr		1486816	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.447197	0.01089	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000425083	D;D;D;D;D;D;D	0.92048	-2.96;-2.96;-2.96;-2.96;-2.96;-2.96;-2.96	4.4	-4.85	0.03142	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	1.607860	0.03854	N	0.272829	T	0.76241	0.3960	N	0.05306	-0.075	0.22330	N	0.99919	B;B;B	0.16166	0.007;0.006;0.016	B;B;B	0.10450	0.005;0.002;0.005	T	0.73332	-0.4016	10	0.02654	T	1	-1.8919	3.9596	0.09405	0.434:0.0:0.3159:0.2501	.	653;769;826	P07202-5;P07202-2;P07202	.;.;PERT_HUMAN	T	826;826;653;826;769;653;47	ENSP00000337263:A826T;ENSP00000318820:A826T;ENSP00000332044:A653T;ENSP00000329869:A826T;ENSP00000371636:A769T;ENSP00000371633:A653T;ENSP00000389659:A47T	ENSP00000329869:A826T	A	+	1	0	TPO	1486816	0.000000	0.05858	0.002000	0.10522	0.149000	0.21700	-0.452000	0.06787	-1.025000	0.03334	0.297000	0.19635	GCG		0.577	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
SAP130	79595	broad.mit.edu	37	2	128774093	128774093	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:128774093C>T	ENST00000259235.3	-	4	584	c.455G>A	c.(454-456)cGt>cAt	p.R152H	SAP130_ENST00000259234.6_Missense_Mutation_p.R126H|SAP130_ENST00000357702.5_Missense_Mutation_p.R152H	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	152	Pro-rich.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.R152H(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		AGCAATGGGACGGCTAGGCAT	0.527																																					p.R152H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G455A	2						.						96.0	96.0	96.0					2																	128774093		2203	4300	6503	128490563	SO:0001583	missense	79595	exon4			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.455G>A	2.37:g.128774093C>T	ENSP00000259235:p.Arg152His		128490563	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.795002	0.90453	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234;ENST00000424298	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.74015	0.3661	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.996	T	0.72574	-0.4252	9	0.52906	T	0.07	-14.4684	20.6439	0.99570	0.0:1.0:0.0:0.0	.	152;126;152	B7ZLM3;Q96DP1;Q9H0E3	.;.;SP130_HUMAN	H	152;152;126;126	.	ENSP00000259234:R126H	R	-	2	0	SAP130	128490563	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.323000	0.79105	2.884000	0.98904	0.655000	0.94253	CGT		0.527	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
ABCA12	26154	broad.mit.edu	37	2	215839577	215839577	+	Missense_Mutation	SNP	G	G	A	rs181314573	byFrequency	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:215839577G>A	ENST00000272895.7	-	35	5612	c.5393C>T	c.(5392-5394)cCg>cTg	p.P1798L	ABCA12_ENST00000389661.4_Missense_Mutation_p.P1480L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1798			P -> L (in ARCI4A; skin phenotype consistent with non-bullous congenital ichthyosiform erythroderma). {ECO:0000269|PubMed:19262603}.		cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.P1798L(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTCCGTGCTCGGGTGATAATT	0.388													G|||	2	0.000399361	0.0	0.0	5008	,	,		19618	0.002		0.0	False		,,,				2504	0.0				p.P1798L	Ovarian(66;664 1488 5121 34295)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5393T	2						.						135.0	136.0	135.0					2																	215839577		2203	4300	6503	215547822	SO:0001583	missense	26154	exon35			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5393C>T	2.37:g.215839577G>A	ENSP00000272895:p.Pro1798Leu		215547822	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.45	1.354712	0.24512	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.90955	-2.76;-2.73	5.7	5.7	0.88788	.	0.491336	0.20666	N	0.087938	D	0.90277	0.6959	M	0.82323	2.585	0.80722	D	1	P;P	0.42757	0.789;0.571	B;B	0.37601	0.254;0.079	D	0.91227	0.5011	10	0.72032	D	0.01	.	12.4432	0.55637	0.0:0.0:0.7901:0.2098	.	1798;1480	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	L	1798;1480	ENSP00000272895:P1798L;ENSP00000374312:P1480L	ENSP00000272895:P1798L	P	-	2	0	ABCA12	215547822	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	2.416000	0.44644	2.705000	0.92388	0.650000	0.86243	CCG		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
SLC23A3	151295	broad.mit.edu	37	2	220026654	220026654	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:220026654C>T	ENST00000409878.3	-	12	1842	c.1810G>A	c.(1810-1812)Gaa>Aaa	p.E604K	SLC23A3_ENST00000396775.3_3'UTR|NHEJ1_ENST00000356853.5_5'Flank|SLC23A3_ENST00000455516.2_Missense_Mutation_p.E612K|SLC23A3_ENST00000295738.7_Missense_Mutation_p.E487K	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	604					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.E487K(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTAAACCCTTCTCTGCTAGAT	0.542																																					p.E612K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1834A	2						.						54.0	52.0	53.0					2																	220026654		1877	4108	5985	219734898	SO:0001583	missense	151295	exon12			BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"""Solute carriers"""	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.1810G>A	2.37:g.220026654C>T	ENSP00000386473:p.Glu604Lys		219734898	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Missense_Mutation	SNP	ENST00000409878.3	37	CCDS46518.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780937	0.70222	.	.	ENSG00000213901	ENST00000295738;ENST00000409878;ENST00000455516	T;T;T	0.52057	0.68;2.13;2.11	3.19	2.28	0.28536	.	0.387149	0.19060	N	0.123784	T	0.27524	0.0676	N	0.24115	0.695	0.20703	N	0.999867	B;B;P	0.36535	0.421;0.421;0.557	B;B;B	0.29785	0.034;0.034;0.107	T	0.08953	-1.0697	9	.	.	.	.	9.9446	0.41600	0.0:0.7909:0.2091:0.0	.	604;612;487	Q6PIS1;B7Z512;Q6PIS1-2	S23A3_HUMAN;.;.	K	487;604;612	ENSP00000295738:E487K;ENSP00000386473:E604K;ENSP00000406546:E612K	.	E	-	1	0	SLC23A3	219734898	0.002000	0.14202	0.116000	0.21606	0.654000	0.38779	0.438000	0.21559	0.880000	0.35969	0.561000	0.74099	GAA		0.542	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712	
PRR21	643905	broad.mit.edu	37	2	240981668	240981668	+	Silent	SNP	C	C	A	rs199598022	byFrequency	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:240981668C>A	ENST00000408934.1	-	1	731	c.732G>T	c.(730-732)acG>acT	p.T244T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	244	Pro-rich.							p.T244T(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GACGAAGGGCCGTGGGTGAAG	0.642													c|||	752	0.15016	0.1861	0.1138	5008	,	,		9753	0.1012		0.1431	False		,,,				2504	0.1851				p.T244T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G732T	2						.						1.0	1.0	1.0					2																	240981668		446	864	1310	240630341	SO:0001819	synonymous_variant	643905	exon1			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.732G>T	2.37:g.240981668C>A			240630341	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																				0.642	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
NRXN1	9378	broad.mit.edu	37	2	50724551	50724551	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:50724551G>T	ENST00000406316.2	-	14	4275	c.2799C>A	c.(2797-2799)ttC>ttA	p.F933L	NRXN1_ENST00000401710.1_5'Flank|NRXN1_ENST00000402717.3_Missense_Mutation_p.F925L|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000405472.3_Missense_Mutation_p.F925L|NRXN1_ENST00000401669.2_Missense_Mutation_p.F933L|NRXN1_ENST00000404971.1_Missense_Mutation_p.F973L|NRXN1_ENST00000406859.3_Missense_Mutation_p.F933L	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	933	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.F974L(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATGTTGTCTTGAACTGGAAAA	0.398																																					p.F973L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2919A	2						.						108.0	101.0	103.0					2																	50724551		1891	4128	6019	50578055	SO:0001583	missense	9378	exon15			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.2799C>A	2.37:g.50724551G>T	ENSP00000384311:p.Phe933Leu		50578055	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.571784	0.65765	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	D;D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21;-2.21	5.58	2.59	0.31030	.	0.000000	0.85682	D	0.000000	D	0.90494	0.7022	M	0.66506	2.035	0.38240	D	0.941297	D;D;D	0.65815	0.984;0.995;0.97	P;P;P	0.62298	0.747;0.847;0.9	D	0.90417	0.4414	10	0.66056	D	0.02	.	11.0009	0.47604	0.2143:0.0:0.7857:0.0	.	973;933;925	Q9ULB1-3;F8WB18;A7E294	.;.;.	L	973;933;925;933;974;925;933	ENSP00000385142:F973L;ENSP00000384311:F933L;ENSP00000434015:F925L;ENSP00000385017:F933L;ENSP00000385434:F925L;ENSP00000385681:F933L	ENSP00000385017:F933L	F	-	3	2	NRXN1	50578055	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.352000	0.52239	0.371000	0.24564	-0.150000	0.13652	TTC		0.398	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
USP34	9736	broad.mit.edu	37	2	61456113	61456113	+	Missense_Mutation	SNP	G	G	T	rs368019041		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:61456113G>T	ENST00000398571.2	-	60	7293	c.7217C>A	c.(7216-7218)aCc>aAc	p.T2406N		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2406					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTCTACTGAGGTATCCATATC	0.358																																					p.T2406N												.	.	0			c.C7217A	2						.						71.0	68.0	69.0					2																	61456113		1853	4096	5949	61309617	SO:0001583	missense	9736	exon60			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.7217C>A	2.37:g.61456113G>T	ENSP00000381577:p.Thr2406Asn		61309617	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.24|15.24	2.774741|2.774741	0.49786|0.49786	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734|ENST00000411912	T;T|.	0.03982|.	3.94;3.74|.	6.17|6.17	5.28|5.28	0.74379|0.74379	Armadillo-type fold (1);|.	0.143844|.	0.64402|.	D|.	0.000006|.	T|.	0.20088|.	0.0483|.	N|N	0.03608|0.03608	-0.345|-0.345	0.22968|0.22968	N|N	0.998493|0.998493	B|.	0.02656|.	0.0|.	B|.	0.08055|.	0.003|.	T|.	0.13629|.	-1.0502|.	10|.	0.27082|.	T|.	0.32|.	.|.	13.7253|13.7253	0.62754|0.62754	0.0:0.3557:0.6443:0.0|0.0:0.3557:0.6443:0.0	.|.	2406|.	Q70CQ2|.	UBP34_HUMAN|.	N|X	2254;2254;2406;684|165	ENSP00000381577:T2406N;ENSP00000410559:T684N|.	ENSP00000263989:T2254N|.	T|Y	-|-	2|3	0|2	USP34|USP34	61309617|61309617	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.921000|0.921000	0.55340|0.55340	4.461000|4.461000	0.60115|0.60115	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	ACC|TAC		0.358	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
ZNF638	27332	broad.mit.edu	37	2	71576741	71576741	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:71576741C>A	ENST00000409544.1	+	2	1287	c.657C>A	c.(655-657)taC>taA	p.Y219*	ZNF638_ENST00000377802.2_Nonsense_Mutation_p.Y219*|ZNF638_ENST00000264447.4_Nonsense_Mutation_p.Y219*|ZNF638_ENST00000355812.3_Nonsense_Mutation_p.Y219*|ZNF638_ENST00000410075.1_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	219					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AATATGGCTACACAGAAGATC	0.383																																					p.Y219X												.	.	0			c.C657A	2						.						101.0	97.0	99.0					2																	71576741		2203	4300	6503	71430249	SO:0001587	stop_gained	27332	exon2			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.657C>A	2.37:g.71576741C>A	ENSP00000386433:p.Tyr219*		71430249	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Nonsense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	38	7.121135	0.98077	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	.	.	.	5.84	4.03	0.46877	.	0.137689	0.50627	D	0.000120	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5945	7.4251	0.27094	0.0:0.7355:0.0:0.2645	.	.	.	.	X	219;325;219;219;219;219	.	ENSP00000264447:Y219X	Y	+	3	2	ZNF638	71430249	0.999000	0.42202	1.000000	0.80357	0.981000	0.71138	1.051000	0.30417	0.793000	0.33875	0.655000	0.94253	TAC		0.383	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
KIF1A	547	broad.mit.edu	37	2	241697823	241697823	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr2:241697823C>T	ENST00000320389.7	-	25	2667	c.2509G>A	c.(2509-2511)Gga>Aga	p.G837R	KIF1A_ENST00000498729.2_Missense_Mutation_p.G846R	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	837					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.G837R(1)		NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		AAGGGGTCTCCGCCGGTCACC	0.632																																					p.G837R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2509A	2						.						56.0	66.0	63.0					2																	241697823		2149	4250	6399	241346496	SO:0001583	missense	547	exon25			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2509G>A	2.37:g.241697823C>T	ENSP00000322791:p.Gly837Arg		241346496	NM_004321	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727943	0.89390	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.75704	-0.96;-0.96;-0.96	5.28	5.28	0.74379	.	0.000000	0.85682	U	0.000000	T	0.81202	0.4773	L	0.36672	1.1	0.80722	D	1	D;D;B	0.89917	0.98;1.0;0.015	P;D;B	0.79108	0.759;0.992;0.031	T	0.80754	-0.1241	10	0.42905	T	0.14	.	18.4813	0.90812	0.0:1.0:0.0:0.0	.	846;846;837	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	R	837;846;846;846	ENSP00000322791:G837R;ENSP00000438388:G846R;ENSP00000384231:G846R	ENSP00000322791:G837R	G	-	1	0	KIF1A	241346496	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	4.679000	0.61649	2.473000	0.83533	0.591000	0.81541	GGA		0.632	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
PODXL2	50512	broad.mit.edu	37	3	127387302	127387303	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:127387302_127387303insG	ENST00000342480.6	+	5	1264_1265	c.1225_1226insG	c.(1225-1227)cggfs	p.R409fs		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	409					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						CCGGCAGCACCGGGGGCCACAG	0.653																																					p.R409fs												.	.	0			c.1225_1226insG	3						.																																			128869993	SO:0001589	frameshift_variant	50512	exon5			AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.1230dupG	3.37:g.127387307_127387307dupG	ENSP00000345359:p.Arg409fs		128869992	NM_015720	Q6UVY4|Q8WUV6	Frame_Shift_Ins	INS	ENST00000342480.6	37	CCDS3044.1																																																																																				0.653	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
IQCB1	9657	broad.mit.edu	37	3	121547423	121547424	+	Missense_Mutation	DNP	TA	TA	CC	rs542335278		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	TA	TA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:121547423_121547424TA>CC	ENST00000310864.6	-	4	370_371	c.156_157TA>GG	c.(154-159)gaTAta>gaGGta	p.52_53DI>EV	IQCB1_ENST00000349820.6_Missense_Mutation_p.52_53DI>EV	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	52					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)	p.D52>?(1)		NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TAACAATATATATCTTGTTTGA	0.327																																					.												.	.	1	Complex(1)	large_intestine(1)	c.156_157GG	3						.																																			123030114	SO:0001583	missense	9657	exon4			D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.156_157delinsCC	3.37:g.121547423_121547424delinsCC	ENSP00000311505:p.D52_I53delinsEV		123030113	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	DNP	ENST00000310864.6	37	CCDS33837.1																																																																																				0.327	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
COL6A6	131873	broad.mit.edu	37	3	130289967	130289967	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:130289967C>T	ENST00000358511.6	+	6	2738	c.2707C>T	c.(2707-2709)Cgg>Tgg	p.R903W	COL6A6_ENST00000453409.2_Missense_Mutation_p.R903W	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	903	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.R903W(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CACTGAAGCCCGGGGCAGCCG	0.542																																					p.R903W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2707T	3						.						39.0	41.0	40.0					3																	130289967		1879	4093	5972	131772657	SO:0001583	missense	131873	exon6			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2707C>T	3.37:g.130289967C>T	ENSP00000351310:p.Arg903Trp		131772657	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	15.28	2.787741	0.49997	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.84298	-1.83;-1.83	4.92	2.0	0.26442	von Willebrand factor, type A (3);	0.261718	0.27202	N	0.020443	T	0.79799	0.4508	M	0.67569	2.06	0.24486	N	0.994322	B	0.06786	0.001	B	0.06405	0.002	T	0.66991	-0.5783	10	0.38643	T	0.18	.	5.6574	0.17650	0.3905:0.4609:0.0:0.1487	.	903	A6NMZ7	CO6A6_HUMAN	W	903	ENSP00000351310:R903W;ENSP00000399236:R903W	ENSP00000351310:R903W	R	+	1	2	COL6A6	131772657	0.000000	0.05858	0.997000	0.53966	0.958000	0.62258	-0.658000	0.05329	0.181000	0.19994	0.561000	0.74099	CGG		0.542	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
RARB	5915	broad.mit.edu	37	3	25542766	25542766	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:25542766C>G	ENST00000404969.1	+	3	421	c.421C>G	c.(421-423)Caa>Gaa	p.Q141E	RARB_ENST00000458646.1_Missense_Mutation_p.Q22E|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000330688.4_Missense_Mutation_p.Q134E|RARB_ENST00000437042.2_Missense_Mutation_p.Q22E			P10826	RARB_HUMAN	retinoic acid receptor, beta	141					embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.Q134E(1)|p.Q141E(1)		breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GAATCGATGCCAATACTGTCG	0.388																																					p.Q134E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C400G	3						.						107.0	107.0	107.0					3																	25542766		2203	4300	6503	25517770	SO:0001583	missense	5915	exon3			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.421C>G	3.37:g.25542766C>G	ENSP00000385865:p.Gln141Glu		25517770	NM_000965	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	C	23.0	4.364977	0.82463	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000437042;ENST00000330688;ENST00000458646	D;D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42;-4.42	4.83	4.83	0.62350	Nuclear hormone receptor, ligand-binding (2);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.98185	0.9400	H	0.96460	3.825	0.80722	D	1	B;B	0.27166	0.17;0.058	B;B	0.36186	0.219;0.103	D	0.99478	1.0947	10	0.72032	D	0.01	.	17.924	0.88977	0.0:1.0:0.0:0.0	.	141;134	P10826;F1D8S6	RARB_HUMAN;.	E	141;141;141;22;134;22	ENSP00000373282:Q141E;ENSP00000385865:Q141E;ENSP00000398840:Q22E;ENSP00000332296:Q134E;ENSP00000391391:Q22E	ENSP00000332296:Q134E	Q	+	1	0	RARB	25517770	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.209000	0.71365	0.650000	0.86243	CAA		0.388	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152	
POMGNT2	84892	broad.mit.edu	37	3	43122251	43122251	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:43122251G>A	ENST00000344697.2	-	2	1018	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R225W	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	225					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)	p.R225W(1)									CACAGCAGCCGGCCCAGGGTC	0.612																																					p.R225W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673T	3						.						48.0	53.0	52.0					3																	43122251		2203	4300	6503	43097255	SO:0001583	missense	84892	exon2			AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.673C>T	3.37:g.43122251G>A	ENSP00000344125:p.Arg225Trp		43097255	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.656077	0.47467	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.78707	-1.2;-1.2	5.69	3.85	0.44370	.	0.052325	0.64402	D	0.000001	T	0.80701	0.4673	L	0.59436	1.845	0.45594	D	0.998539	D	0.69078	0.997	P	0.60609	0.877	T	0.80491	-0.1359	10	0.66056	D	0.02	-23.6443	5.4619	0.16622	0.0704:0.1189:0.5759:0.2348	.	225	Q8NAT1	AGO61_HUMAN	W	225	ENSP00000408992:R225W;ENSP00000344125:R225W	ENSP00000344125:R225W	R	-	1	2	C3orf39	43097255	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.788000	0.38714	1.407000	0.46875	-0.137000	0.14449	CGG		0.612	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
IL17RD	54756	broad.mit.edu	37	3	57131679	57131679	+	Silent	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:57131679C>T	ENST00000296318.7	-	12	2140	c.2052G>A	c.(2050-2052)acG>acA	p.T684T	IL17RD_ENST00000320057.5_Silent_p.T540T|IL17RD_ENST00000463523.1_Silent_p.T540T|IL17RD_ENST00000427856.2_Silent_p.T660T	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	684					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T540T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		CTGTCTGGTCCGTCGAGAGTC	0.617																																					p.T684T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2052A	3						.						45.0	37.0	40.0					3																	57131679		2203	4300	6503	57106719	SO:0001819	synonymous_variant	54756	exon12			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"""Interleukins and interleukin receptors"""	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.2052G>A	3.37:g.57131679C>T			57106719	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	37	CCDS2880.2																																																																																				0.617	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
CLDN18	51208	broad.mit.edu	37	3	137729227	137729227	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr3:137729227G>A	ENST00000183605.5	+	1	386	c.160G>A	c.(160-162)Gtg>Atg	p.V54M	CLDN18_ENST00000343735.4_Intron	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	54					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.V54M(1)		endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						GAGGAGCTGCGTGAGGCAGAG	0.622																																					p.V54M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G160A	3						.						77.0	70.0	72.0					3																	137729227		2203	4300	6503	139211917	SO:0001583	missense	51208	exon1			AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"""Claudins"""	2039	protein-coding gene	gene with protein product		609210	"""surfactant associated protein J"""	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.160G>A	3.37:g.137729227G>A	ENSP00000183605:p.Val54Met		139211917	NM_016369	A5PL21|Q96PH4	Missense_Mutation	SNP	ENST00000183605.5	37	CCDS3095.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085341	0.76642	.	.	ENSG00000066405	ENST00000183605;ENST00000536138	D	0.89939	-2.59	5.55	4.68	0.58851	Claudin, conserved site (1);	.	.	.	.	D	0.93919	0.8054	M	0.77406	2.37	0.46185	D	0.998914	D	0.89917	1.0	D	0.76071	0.987	D	0.94337	0.7567	9	0.66056	D	0.02	.	14.2433	0.65971	0.0715:0.0:0.9285:0.0	.	54	P56856	CLD18_HUMAN	M	54	ENSP00000183605:V54M	ENSP00000183605:V54M	V	+	1	0	CLDN18	139211917	1.000000	0.71417	0.883000	0.34634	0.943000	0.58893	6.636000	0.74299	1.351000	0.45789	0.467000	0.42956	GTG		0.622	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026	
ANK2	287	broad.mit.edu	37	4	114260394	114260394	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:114260394C>A	ENST00000357077.4	+	32	3862	c.3809C>A	c.(3808-3810)cCt>cAt	p.P1270H	ANK2_ENST00000506722.1_Missense_Mutation_p.P1261H|ANK2_ENST00000394537.3_Missense_Mutation_p.P1270H|ANK2_ENST00000504887.1_3'UTR|ANK2_ENST00000264366.6_Missense_Mutation_p.P1237H|ANK2_ENST00000510275.2_5'Flank|ANK2_ENST00000509550.1_Missense_Mutation_p.P446H	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1270	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.P1270H(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GGAACCACCCCTGCCCAGTGG	0.383																																					p.P1270H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3809A	4						.						113.0	109.0	111.0					4																	114260394		2203	4300	6503	114479843	SO:0001583	missense	287	exon32			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.3809C>A	4.37:g.114260394C>A	ENSP00000349588:p.Pro1270His		114479843	NM_020977	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646903	0.87958	.	.	ENSG00000145362	ENST00000503423;ENST00000506722;ENST00000431447;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.1	5.1	0.69264	.	0.000000	0.50627	D	0.000118	T	0.62122	0.2402	M	0.85542	2.76	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.997;0.999;0.999;0.997;1.0;0.997	T	0.69101	-0.5234	10	0.72032	D	0.01	.	18.5418	0.91031	0.0:1.0:0.0:0.0	.	446;1237;282;1270;1270;1261	E9PCH6;Q01484;Q7Z344;Q01484-2;Q01484-4;Q01484-5	.;ANK2_HUMAN;.;.;.;.	H	1183;1261;316;1285;1270;1270;1237;1261;446	ENSP00000421011:P1183H;ENSP00000421067:P1261H;ENSP00000424722:P1285H;ENSP00000378044:P1270H;ENSP00000349588:P1270H;ENSP00000264366:P1237H;ENSP00000426944:P446H	ENSP00000264366:P1237H	P	+	2	0	ANK2	114479843	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.082000	0.71318	2.369000	0.80426	0.591000	0.81541	CCT		0.383	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
FAT4	79633	broad.mit.edu	37	4	126238182	126238182	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:126238182G>C	ENST00000394329.3	+	1	629	c.616G>C	c.(616-618)Ggc>Cgc	p.G206R		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	206	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G206R(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGTGTCCAAGGGCGGACTGGA	0.637											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G206R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G616C	4						.						44.0	51.0	49.0					4																	126238182		2100	4224	6324	126457632	SO:0001583	missense	79633	exon1			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.616G>C	4.37:g.126238182G>C	ENSP00000377862:p.Gly206Arg	1548	126457632	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315960	0.60524	.	.	ENSG00000196159	ENST00000394329	T	0.49432	0.78	5.31	5.31	0.75309	Cadherin (4);Cadherin-like (1);	0.000000	0.35067	U	0.003472	T	0.55194	0.1905	L	0.39245	1.2	0.80722	D	1	D	0.59767	0.986	D	0.69307	0.963	T	0.45848	-0.9233	10	0.20046	T	0.44	.	12.3581	0.55186	0.077:0.0:0.923:0.0	.	206	Q6V0I7	FAT4_HUMAN	R	206	ENSP00000377862:G206R	ENSP00000377862:G206R	G	+	1	0	FAT4	126457632	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	6.597000	0.74118	2.467000	0.83353	0.655000	0.94253	GGC		0.637	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126238318	126238318	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:126238318G>A	ENST00000394329.3	+	1	765	c.752G>A	c.(751-753)gGc>gAc	p.G251D		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	251	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G251D(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCGGTTTTTGGCAGTTCTCAC	0.632											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G251D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G752A	4						.						23.0	27.0	25.0					4																	126238318		1947	4146	6093	126457768	SO:0001583	missense	79633	exon1			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.752G>A	4.37:g.126238318G>A	ENSP00000377862:p.Gly251Asp	1548	126457768	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	0.065	-1.215088	0.01542	.	.	ENSG00000196159	ENST00000394329	T	0.60548	0.18	5.13	3.39	0.38822	Cadherin (3);Cadherin-like (1);	0.206931	0.23300	U	0.049700	T	0.26666	0.0652	N	0.03194	-0.395	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.06625	-1.0816	10	0.09590	T	0.72	.	6.6454	0.22933	0.1569:0.1478:0.6954:0.0	.	251	Q6V0I7	FAT4_HUMAN	D	251	ENSP00000377862:G251D	ENSP00000377862:G251D	G	+	2	0	FAT4	126457768	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	5.001000	0.63946	1.139000	0.42245	0.655000	0.94253	GGC		0.632	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CCKAR	886	broad.mit.edu	37	4	26491094	26491094	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:26491094G>A	ENST00000295589.3	-	2	319	c.125C>T	c.(124-126)gCg>gTg	p.A42V		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	42					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)	p.A42V(1)		NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	AATCTGCACCGCTGGCTGCCA	0.547																																					p.A42V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C125T	4						.						54.0	59.0	57.0					4																	26491094		2203	4300	6503	26100192	SO:0001583	missense	886	exon2			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"""GPCR / Class A : Cholecystokinin receptors"""	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.125C>T	4.37:g.26491094G>A	ENSP00000295589:p.Ala42Val		26100192	NM_000730	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.917801	0.52546	.	.	ENSG00000163394	ENST00000295589	T	0.35048	1.33	5.24	4.39	0.52855	Cholecystokinin A receptor, N-terminal (1);	0.129659	0.49916	D	0.000130	T	0.32285	0.0824	M	0.69823	2.125	0.37804	D	0.9278	P	0.40398	0.716	B	0.37198	0.243	T	0.18493	-1.0335	10	0.10902	T	0.67	.	10.5652	0.45169	0.1471:0.0:0.8529:0.0	.	42	P32238	CCKAR_HUMAN	V	42	ENSP00000295589:A42V	ENSP00000295589:A42V	A	-	2	0	CCKAR	26100192	1.000000	0.71417	0.469000	0.27204	0.894000	0.52154	5.721000	0.68477	2.445000	0.82738	0.561000	0.74099	GCG		0.547	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2		
TMPRSS11A	339967	broad.mit.edu	37	4	68784789	68784789	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:68784789G>A	ENST00000334830.7	-	8	1609	c.863C>T	c.(862-864)tCg>tTg	p.S288L	TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.S284L|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.S285L|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	288	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			S -> P (in Ref. 1; AAD41463). {ECO:0000305}.	cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.S288L(2)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						TATGTCATCCGAAAAGGTGAC	0.443																																					p.S288L	NSCLC(26;2 894 10941 14480 22546)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C863T	4						.						161.0	165.0	163.0					4																	68784789		2203	4300	6503	68467384	SO:0001583	missense	339967	exon8			AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"""Serine peptidases / Transmembrane"""	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.863C>T	4.37:g.68784789G>A	ENSP00000334611:p.Ser288Leu		68467384	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529581	0.44969	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42	5.36	5.36	0.76844	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.113273	0.39341	N	0.001393	D	0.94528	0.8238	M	0.83774	2.66	0.39621	D	0.970031	P;P	0.49862	0.929;0.929	B;B	0.41374	0.355;0.355	D	0.95933	0.8940	10	0.87932	D	0	.	16.5682	0.84604	0.0:0.0:1.0:0.0	.	285;288	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	L	284;288;285;252	ENSP00000426911:S284L;ENSP00000334611:S288L;ENSP00000379491:S285L;ENSP00000427621:S252L	ENSP00000334611:S288L	S	-	2	0	TMPRSS11A	68467384	0.976000	0.34144	0.312000	0.25196	0.086000	0.17979	2.020000	0.41010	2.512000	0.84698	0.591000	0.81541	TCG		0.443	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	
HELQ	113510	broad.mit.edu	37	4	84342878	84342878	+	Silent	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:84342878C>T	ENST00000295488.3	-	15	2949	c.2787G>A	c.(2785-2787)aaG>aaA	p.K929K	HELQ_ENST00000510985.1_Silent_p.K862K	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	929					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.K929K(1)		breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TGACAACGTTCTTGTCCACCT	0.333								Other identified genes with known or suspected DNA repair function																													p.K929K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2787A	4						.						70.0	68.0	69.0					4																	84342878		2203	4300	6503	84561902	SO:0001819	synonymous_variant	113510	exon15			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2787G>A	4.37:g.84342878C>T			84561902	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																				0.333	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
WDFY3	23001	broad.mit.edu	37	4	85645590	85645590	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:85645590G>T	ENST00000295888.4	-	46	7837	c.7430C>A	c.(7429-7431)gCt>gAt	p.A2477D	WDFY3_ENST00000322366.6_Missense_Mutation_p.A2460D	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2477	Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.A2477D(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TTTGACTTTAGCAATAGTGTC	0.413																																					p.A2477D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7430A	4						.						137.0	132.0	134.0					4																	85645590		2203	4300	6503	85864614	SO:0001583	missense	23001	exon46			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.7430C>A	4.37:g.85645590G>T	ENSP00000295888:p.Ala2477Asp		85864614	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927270	0.34002	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.64803	-0.06;-0.12;-0.07	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	L	0.34521	1.04	0.80722	D	1	B	0.19073	0.033	B	0.16289	0.015	T	0.44982	-0.9292	10	0.21540	T	0.41	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	2477	Q8IZQ1	WDFY3_HUMAN	D	2460;2477;80	ENSP00000318466:A2460D;ENSP00000295888:A2477D;ENSP00000424987:A80D	ENSP00000295888:A2477D	A	-	2	0	WDFY3	85864614	1.000000	0.71417	0.982000	0.44146	0.344000	0.29017	7.954000	0.87848	2.885000	0.99019	0.655000	0.94253	GCT		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
FAT4	79633	broad.mit.edu	37	4	126328099	126328099	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr4:126328099C>A	ENST00000394329.3	+	3	5385	c.5372C>A	c.(5371-5373)cCa>cAa	p.P1791Q	FAT4_ENST00000335110.5_Missense_Mutation_p.P89Q	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1791	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1791Q(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CGCATCGACCCAGAATCCGGA	0.478																																					p.P1791Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5372A	4						.						128.0	121.0	123.0					4																	126328099		2203	4300	6503	126547549	SO:0001583	missense	79633	exon3			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5372C>A	4.37:g.126328099C>A	ENSP00000377862:p.Pro1791Gln		126547549	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205651	0.79127	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01705	4.68;4.68	5.28	5.28	0.74379	Cadherin (4);Cadherin-like (1);	0.000000	0.34362	U	0.004027	T	0.09423	0.0232	L	0.60067	1.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.02603	-1.1135	10	0.52906	T	0.07	.	19.2767	0.94034	0.0:1.0:0.0:0.0	.	89;1791	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	Q	1791;89	ENSP00000377862:P1791Q;ENSP00000335169:P89Q	ENSP00000335169:P89Q	P	+	2	0	FAT4	126547549	1.000000	0.71417	0.974000	0.42286	0.529000	0.34654	7.428000	0.80296	2.622000	0.88805	0.585000	0.79938	CCA		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
WDR36	134430	broad.mit.edu	37	5	110428028	110428028	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr5:110428028G>T	ENST00000513710.2	+	1	46	c.42G>T	c.(40-42)caG>caT	p.Q14H	WDR36_ENST00000506538.2_Missense_Mutation_p.Q14H|WDR36_ENST00000505303.1_5'UTR|CTC-551A13.2_ENST00000507269.3_RNA			Q8NI36	WDR36_HUMAN	WD repeat domain 36	14					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)	p.Q14H(1)		cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GCGATTCGCAGCGGGCGCCGG	0.592																																					p.Q14H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G42T	5						.						78.0	85.0	82.0					5																	110428028		2202	4300	6502	110455927	SO:0001583	missense	134430	exon1			AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.42G>T	5.37:g.110428028G>T	ENSP00000424628:p.Gln14His		110455927	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	37	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780849	0.49891	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.66995	-0.24;-0.24	5.0	3.11	0.35812	.	0.747484	0.11517	N	0.556135	T	0.48502	0.1503	N	0.08118	0	0.26325	N	0.9776	B	0.02656	0.0	B	0.01281	0.0	T	0.46289	-0.9202	10	0.87932	D	0	-0.575	12.967	0.58490	0.0:0.3245:0.6755:0.0	.	14	Q8NI36	WDR36_HUMAN	H	14	ENSP00000423067:Q14H;ENSP00000424628:Q14H	ENSP00000423067:Q14H	Q	+	3	2	WDR36	110455927	0.001000	0.12720	0.014000	0.15608	0.588000	0.36517	0.767000	0.26575	0.701000	0.31803	0.655000	0.94253	CAG		0.592	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
APC	324	broad.mit.edu	37	5	112175696	112175696	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr5:112175696C>T	ENST00000457016.1	+	16	4785	c.4405C>T	c.(4405-4407)Caa>Taa	p.Q1469*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1469*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1469*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1469	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1469*(6)|p.A1470fs*17(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGGACCTAAGCAAGCTGCAGT	0.438		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.Q1451X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,NS,Substitution - Nonsense,0 	.	10	Substitution - Nonsense(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	large_intestine(6)|soft_tissue(2)|thyroid(1)|skin(1)	c.C4351T	5						.						81.0	78.0	79.0					5																	112175696		2202	4300	6502	112203595	SO:0001587	stop_gained	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4405C>T	5.37:g.112175696C>T	ENSP00000413133:p.Gln1469*		112203595	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.347607	0.98772	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.16	6.16	0.99307	.	0.300318	0.37530	N	0.002053	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.1458	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	1469	.	.	Q	+	1	0	APC	112203595	1.000000	0.71417	0.997000	0.53966	0.718000	0.41266	6.223000	0.72257	2.937000	0.99478	0.650000	0.86243	CAA		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
DNAH5	1767	broad.mit.edu	37	5	13839485	13839485	+	Silent	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr5:13839485T>C	ENST00000265104.4	-	35	5966	c.5862A>G	c.(5860-5862)gtA>gtG	p.V1954V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1954	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V1954V(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTGGAGTTATTACAAGCCTGT	0.413									Kartagener syndrome																												p.V1954V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5862G	5						.						126.0	129.0	128.0					5																	13839485		2203	4300	6503	13892485	SO:0001819	synonymous_variant	1767	exon35	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5862A>G	5.37:g.13839485T>C			13892485	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ACSL6	23305	broad.mit.edu	37	5	131325149	131325149	+	Missense_Mutation	SNP	T	T	A	rs373520930		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr5:131325149T>A	ENST00000379240.1	-	5	581	c.428A>T	c.(427-429)aAa>aTa	p.K143I	ACSL6_ENST00000357096.1_Missense_Mutation_p.K108I|ACSL6_ENST00000543479.1_Missense_Mutation_p.K143I|ACSL6_ENST00000379272.2_Missense_Mutation_p.K143I|ACSL6_ENST00000296869.4_Missense_Mutation_p.K168I|ACSL6_ENST00000379255.1_Missense_Mutation_p.K108I|ACSL6_ENST00000544770.1_Missense_Mutation_p.K52I|ACSL6_ENST00000379244.1_Missense_Mutation_p.K143I|ACSL6_ENST00000379249.3_Missense_Mutation_p.K143I|ACSL6_ENST00000431707.1_Missense_Mutation_p.K108I|ACSL6_ENST00000379264.2_Missense_Mutation_p.K168I|ACSL6_ENST00000379246.1_Missense_Mutation_p.K154I			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	143					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)	p.K168I(2)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTGCATGCTTTACAATTGTG	0.498																																					p.K168I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A503T	5						.						149.0	151.0	151.0					5																	131325149		2203	4300	6503	131353048	SO:0001583	missense	23305	exon5			AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"""Acyl-CoA synthetase family"""	16496	protein-coding gene	gene with protein product		604443	"""fatty-acid-Coenzyme A ligase, long-chain 6"""	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.428A>T	5.37:g.131325149T>A	ENSP00000368542:p.Lys143Ile		131353048	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	37		.	.	.	.	.	.	.	.	.	.	T	11.62	1.693197	0.30052	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403;ENST00000419502;ENST00000416557	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;2.65;2.65	5.28	5.28	0.74379	AMP-dependent synthetase/ligase (1);	0.145260	0.64402	D	0.000007	T	0.53562	0.1804	M	0.81802	2.56	0.48762	D	0.999708	B;B;B;B;B;B;B	0.12630	0.001;0.004;0.006;0.006;0.001;0.004;0.001	B;B;B;B;B;B;B	0.20577	0.009;0.017;0.02;0.03;0.012;0.012;0.017	T	0.55952	-0.8059	10	0.59425	D	0.04	.	15.2148	0.73258	0.0:0.0:0.0:1.0	.	143;143;133;143;108;168;168	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	I	143;168;143;108;108;168;154;143;52;143;108;143;108;143;143;143	ENSP00000368551:K143I;ENSP00000368566:K168I;ENSP00000368574:K143I;ENSP00000349608:K108I;ENSP00000368557:K108I;ENSP00000296869:K168I;ENSP00000368548:K154I;ENSP00000368546:K143I;ENSP00000445154:K52I;ENSP00000368542:K143I;ENSP00000413329:K108I;ENSP00000442124:K143I;ENSP00000397507:K108I;ENSP00000398423:K143I;ENSP00000388424:K143I;ENSP00000398381:K143I	ENSP00000296869:K168I	K	-	2	0	ACSL6	131353048	1.000000	0.71417	0.997000	0.53966	0.052000	0.14988	3.371000	0.52379	2.008000	0.58898	0.379000	0.24179	AAA		0.498	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256	
BTNL8	79908	broad.mit.edu	37	5	180335598	180335598	+	Missense_Mutation	SNP	T	T	G	rs201214790	byFrequency	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr5:180335598T>G	ENST00000340184.4	+	2	268	c.62T>G	c.(61-63)gTg>gGg	p.V21G	Y_RNA_ENST00000410920.1_RNA|BTNL8_ENST00000231229.4_Missense_Mutation_p.V21G|BTNL8_ENST00000400707.3_Intron|BTNL8_ENST00000505126.1_5'Flank|BTNL8_ENST00000511704.1_Intron|BTNL8_ENST00000508408.1_Missense_Mutation_p.V21G|BTNL8_ENST00000533815.2_5'Flank	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	21	Ig-like V-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.V21G(3)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGTGGCAGGTGTTTGGGCCA	0.547																																					p.V21G												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.T62G	5						.						47.0	49.0	48.0					5																	180335598		2203	4300	6503	180268204	SO:0001583	missense	79908	exon2			AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.62T>G	5.37:g.180335598T>G	ENSP00000342197:p.Val21Gly		180268204	NM_024850	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595570	0.46318	.	.	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000508408	T;T;T	0.72167	-0.63;-0.63;-0.63	2.58	2.58	0.30949	Immunoglobulin V-set (1);	.	.	.	.	D	0.84866	0.5567	M	0.92923	3.36	0.09310	P	0.999999999143561	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87135	0.2199	8	0.87932	D	0	.	6.9269	0.24419	0.0:0.0:0.0:1.0	.	21;21;21	F2Z2B2;A6NEX6;Q6UX41	.;.;BTNL8_HUMAN	G	21	ENSP00000231229:V21G;ENSP00000342197:V21G;ENSP00000424585:V21G	ENSP00000231229:V21G	V	+	2	0	BTNL8	180268204	0.811000	0.29063	0.776000	0.31678	0.071000	0.16799	3.679000	0.54634	1.197000	0.43143	0.358000	0.22013	GTG		0.547	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
RNF182	221687	broad.mit.edu	37	6	13977776	13977776	+	Silent	SNP	G	G	A	rs528284492		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr6:13977776G>A	ENST00000488300.1	+	3	949	c.426G>A	c.(424-426)ccG>ccA	p.P142P	RNF182_ENST00000537388.1_Silent_p.P142P|RNF182_ENST00000537663.1_Silent_p.P142P|RNF182_ENST00000544682.1_Silent_p.P142P	NM_152737.3	NP_689950.1	Q8N6D2	RN182_HUMAN	ring finger protein 182	142					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P142P(1)		cervix(1)|large_intestine(7)|liver(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			AGAGCTCCCCGTCCCTGAGCT	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		19681	0.001		0.0	False		,,,				2504	0.0				p.P142P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G426A	6						.						84.0	87.0	86.0					6																	13977776		2203	4300	6503	14085755	SO:0001819	synonymous_variant	221687	exon4			AK090576	CCDS4531.1	6p23	2013-01-09			ENSG00000180537	ENSG00000180537		"""RING-type (C3HC4) zinc fingers"""	28522	protein-coding gene	gene with protein product						12477932	Standard	NM_152737		Approved	MGC33993	uc003nbg.3	Q8N6D2	OTTHUMG00000014280	ENST00000488300.1:c.426G>A	6.37:g.13977776G>A			14085755	NM_001165032	B2RDG2|Q8NBG3	Silent	SNP	ENST00000488300.1	37	CCDS4531.1																																																																																				0.562	RNF182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039911.2	NM_152737	
FNDC1	84624	broad.mit.edu	37	6	159653636	159653636	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr6:159653636C>T	ENST00000297267.9	+	11	2292	c.2092C>T	c.(2092-2094)Cgg>Tgg	p.R698W	FNDC1_ENST00000340366.6_Missense_Mutation_p.R635W	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	698	Ser-rich.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R698W(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTCGCCGGCCCGGAGGACCCC	0.697																																					p.R698W												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C2092T	6						.						12.0	16.0	15.0					6																	159653636		1913	4107	6020	159573626	SO:0001583	missense	84624	exon11			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2092C>T	6.37:g.159653636C>T	ENSP00000297267:p.Arg698Trp		159573626	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.02|13.02	2.112881|2.112881	0.37242|0.37242	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.08193	.|3.12;3.92	5.29|5.29	-1.31|-1.31	0.09230|0.09230	.|.	.|1.799200	.|0.02615	.|N	.|0.102544	T|T	0.01627|0.01627	0.0052|0.0052	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17465	.|0.022;0.013	.|B;B	.|0.12156	.|0.007;0.003	T|T	0.43925|0.43925	-0.9361|-0.9361	5|10	.|0.46703	.|T	.|0.11	-0.3032|-0.3032	0.6023|0.6023	0.00747|0.00747	0.2737:0.3433:0.1337:0.2492|0.2737:0.3433:0.1337:0.2492	.|.	.|635;698	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	L|W	593|698;635	.|ENSP00000297267:R698W;ENSP00000342460:R635W	.|ENSP00000297267:R698W	P|R	+|+	2|1	0|2	FNDC1|FNDC1	159573626|159573626	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.061000|-0.061000	0.11693|0.11693	-0.665000|-0.665000	0.05317|0.05317	-0.878000|-0.878000	0.02970|0.02970	CCG|CGG		0.697	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
THBS2	7058	broad.mit.edu	37	6	169628312	169628312	+	Missense_Mutation	SNP	C	C	T	rs368102843		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr6:169628312C>T	ENST00000366787.3	-	16	2573	c.2324G>A	c.(2323-2325)cGc>cAc	p.R775H	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	775					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R775H(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GTTGTCACAGCGGTCCCCAAC	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		16529	0.001		0.0	False		,,,				2504	0.0				p.R775H	Esophageal Squamous(91;219 1934 18562 44706)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2324A	6						.	C	HIS/ARG	0,4406		0,0,2203	195.0	153.0	167.0		2324	4.5	1.0	6		167	1,8599	1.2+/-3.3	0,1,4299	no	missense	THBS2	NM_003247.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	775/1173	169628312	1,13005	2203	4300	6503	169370237	SO:0001583	missense	7058	exon16				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2324G>A	6.37:g.169628312C>T	ENSP00000355751:p.Arg775His		169370237	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.880766	0.91740	0.0	1.16E-4	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.97665	-4.48	4.51	4.51	0.55191	.	0.000000	0.41712	U	0.000822	D	0.97420	0.9156	L	0.53617	1.68	0.58432	D	0.999998	D	0.89917	1.0	D	0.70935	0.971	D	0.97454	1.0030	10	0.48119	T	0.1	-65.3644	17.5907	0.87995	0.0:1.0:0.0:0.0	.	775	P35442	TSP2_HUMAN	H	775;33	ENSP00000355751:R775H	ENSP00000355751:R775H	R	-	2	0	THBS2	169370237	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.234000	0.78134	2.211000	0.71520	0.579000	0.79373	CGC		0.552	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
DNAH11	8701	broad.mit.edu	37	7	21675532	21675532	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr7:21675532T>C	ENST00000409508.3	+	26	4575	c.4544T>C	c.(4543-4545)tTc>tCc	p.F1515S	DNAH11_ENST00000465593.1_3'UTR|DNAH11_ENST00000328843.6_Missense_Mutation_p.F1520S	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1520	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.F1520S(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTAGAATATTTCATTGAGCAA	0.363									Kartagener syndrome																												p.F1520S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4559C	7						.						56.0	53.0	54.0					7																	21675532		1838	4082	5920	21642057	SO:0001583	missense	8701	exon26	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4544T>C	7.37:g.21675532T>C	ENSP00000475939:p.Phe1515Ser		21642057	NM_003777	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	25.6	4.651862	0.88056	.	.	ENSG00000105877	ENST00000328843	T	0.67865	-0.29	5.56	5.56	0.83823	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.82300	0.5007	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.85000	0.0899	9	0.87932	D	0	.	14.6877	0.69062	0.0:0.0:0.0:1.0	.	1520	Q96DT5	DYH11_HUMAN	S	1520	ENSP00000330671:F1520S	ENSP00000330671:F1520S	F	+	2	0	DNAH11	21642057	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.428000	0.80296	2.098000	0.63641	0.528000	0.53228	TTC		0.363	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
DNAH11	8701	broad.mit.edu	37	7	21813560	21813560	+	Silent	SNP	C	C	T	rs200160729		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr7:21813560C>T	ENST00000409508.3	+	56	9310	c.9279C>T	c.(9277-9279)tcC>tcT	p.S3093S	DNAH11_ENST00000328843.6_Silent_p.S3100S	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3100	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S3100S(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATGAGGTATCCGAGAAAAAAG	0.393									Kartagener syndrome																												p.R3101X												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9301T	7						.	C		0,3656		0,0,1828	45.0	42.0	43.0		9301	-3.0	0.0	7		43	3,8149		0,3,4073	yes	coding-synonymous	DNAH11	NM_003777.3		0,3,5901	TT,TC,CC		0.0368,0.0,0.0254		3100/4524	21813560	3,11805	1828	4076	5904	21780085	SO:0001819	synonymous_variant	8701	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.9279C>T	7.37:g.21813560C>T			21780085	NM_003777	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																					0.393	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
AUTS2	26053	broad.mit.edu	37	7	70231245	70231245	+	Silent	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr7:70231245G>A	ENST00000342771.4	+	9	1935	c.1614G>A	c.(1612-1614)acG>acA	p.T538T	AUTS2_ENST00000406775.2_Silent_p.T538T	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	538	His-rich.							p.T538T(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		accagcacacgcaccagcaca	0.667																																					p.T538T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1614A	7						.						285.0	265.0	272.0					7																	70231245		2203	4300	6503	69869181	SO:0001819	synonymous_variant	26053	exon9			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1614G>A	7.37:g.70231245G>A			69869181	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	9.515	1.106662	0.20714	.	.	ENSG00000158321	ENST00000443672	.	.	.	5.77	-3.61	0.04556	.	.	.	.	.	T	0.51346	0.1669	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48445	-0.9035	4	.	.	.	-12.9426	8.2381	0.31638	0.495:0.2713:0.2337:0.0	.	.	.	.	H	80	.	.	R	+	2	0	AUTS2	69869181	0.806000	0.28996	0.945000	0.38365	0.993000	0.82548	-0.097000	0.11042	-0.733000	0.04850	-0.459000	0.05422	CGC		0.667	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
CFAP69	79846	broad.mit.edu	37	7	89939424	89939424	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr7:89939424C>T	ENST00000389297.4	+	23	2949	c.2698C>T	c.(2698-2700)Cga>Tga	p.R900*	C7orf63_ENST00000497910.1_Nonsense_Mutation_p.R882*|C7orf63_ENST00000316089.8_Nonsense_Mutation_p.R854*|AC002064.5_ENST00000445784.1_lincRNA	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		900								p.R854R(1)|p.R854*(1)|p.R900R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CACTCCTGCCCGATTAGTAGG	0.428																																					p.R882X												.	.	3	Substitution - coding silent(2)|Substitution - Nonsense(1)	kidney(2)|large_intestine(1)	c.C2644T	7						.						135.0	126.0	129.0					7																	89939424		1886	4109	5995	89777360	SO:0001587	stop_gained	79846	exon23																														ENST00000389297.4:c.2698C>T	7.37:g.89939424C>T	ENSP00000373948:p.Arg900*		89777360	NM_001160138	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Nonsense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.4|23.4	4.409440|4.409440	0.83340|0.83340	.|.	.|.	ENSG00000105792|ENSG00000105792	ENST00000412839;ENST00000445156|ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	.|.	.|.	.|.	5.83|5.83	1.24|1.24	0.21308|0.21308	.|.	.|0.342714	.|0.25411	.|N	.|0.030880	T|.	0.33323|.	0.0859|.	.|.	.|.	.|.	0.51482|0.51482	D|D	0.999926|0.999926	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.04386|.	-1.0955|.	4|.	.|0.09338	.|T	.|0.73	-1.1936|-1.1936	6.4015|6.4015	0.21640|0.21640	0.3183:0.5109:0.1039:0.067|0.3183:0.5109:0.1039:0.067	.|.	.|.	.|.	.|.	L|X	128;51|900;854;882;437	.|.	.|ENSP00000321753:R854X	P|R	+|+	2|1	0|2	C7orf63|C7orf63	89777360|89777360	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.967000|0.967000	0.64934|0.64934	-0.002000|-0.002000	0.12924|0.12924	0.320000|0.320000	0.23234|0.23234	0.655000|0.655000	0.94253|0.94253	CCG|CGA		0.428	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
AASS	10157	broad.mit.edu	37	7	121755213	121755213	+	Silent	SNP	G	G	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr7:121755213G>A	ENST00000393376.1	-	8	1053	c.958C>T	c.(958-960)Cta>Tta	p.L320L	AASS_ENST00000417368.2_Silent_p.L320L|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	320	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.L320L(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TGGCGGGTTAGGAGGCGAGGA	0.468																																					p.L320L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C958T	7						.						133.0	126.0	129.0					7																	121755213		2203	4300	6503	121542449	SO:0001819	synonymous_variant	10157	exon9			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.958C>T	7.37:g.121755213G>A			121542449	NM_005763	O95462	Silent	SNP	ENST00000393376.1	37	CCDS5783.1																																																																																				0.468	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
SLC20A2	6575	broad.mit.edu	37	8	42295091	42295091	+	Silent	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr8:42295091T>C	ENST00000342228.3	-	8	1308	c.939A>G	c.(937-939)agA>agG	p.R313R	SLC20A2_ENST00000520179.1_Silent_p.R313R|SLC20A2_ENST00000520262.1_Silent_p.R313R	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	313					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)	p.R313R(1)		breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			TGGACAGTGCTCTTCCTGAAA	0.507																																					p.R313R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A939G	8						.						56.0	51.0	53.0					8																	42295091		2203	4300	6503	42414248	SO:0001819	synonymous_variant	6575	exon8				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"""Solute carriers"""	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.939A>G	8.37:g.42295091T>C			42414248	NM_006749		Silent	SNP	ENST00000342228.3	37	CCDS6132.1																																																																																				0.507	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1		
COL27A1	85301	broad.mit.edu	37	9	116931259	116931259	+	Missense_Mutation	SNP	G	G	A	rs144241003		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr9:116931259G>A	ENST00000356083.3	+	3	1815	c.1424G>A	c.(1423-1425)cGc>cAc	p.R475H		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	475	Pro-rich.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.R475H(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GCCTCTGCCCGCACCAGCACC	0.572																																					p.R475H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1424A	9						.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	158.0	182.0	174.0		1424	-9.3	0.0	9	dbSNP_134	174	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL27A1	NM_032888.2	29	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	benign	475/1861	116931259	3,13003	2203	4300	6503	115971080	SO:0001583	missense	85301	exon3			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.1424G>A	9.37:g.116931259G>A	ENSP00000348385:p.Arg475His		115971080	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	9.146	1.014975	0.19355	4.54E-4	1.16E-4	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.91740	-2.6;-2.9	4.7	-9.32	0.00643	.	.	.	.	.	T	0.76702	0.4024	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.64698	-0.6346	9	0.13853	T	0.58	.	5.4304	0.16450	0.5879:0.0983:0.2145:0.0993	.	475;422	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	H	475;475;422;422	ENSP00000348385:R475H;ENSP00000391328:R422H	ENSP00000348385:R475H	R	+	2	0	COL27A1	115971080	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-4.109000	0.00293	-1.755000	0.01320	-0.379000	0.06801	CGC		0.572	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
VPS13A	23230	broad.mit.edu	37	9	79820908	79820908	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr9:79820908C>A	ENST00000360280.3	+	5	558	c.298C>A	c.(298-300)Cct>Act	p.P100T	VPS13A_ENST00000376634.4_Missense_Mutation_p.P100T|VPS13A_ENST00000376636.3_Missense_Mutation_p.P100T|VPS13A_ENST00000357409.5_Missense_Mutation_p.P100T	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	100					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.P100T(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAAATATGATCCTTTAAAAGA	0.274																																					p.P100T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C298A	9						.						54.0	54.0	54.0					9																	79820908		2198	4289	6487	79010728	SO:0001583	missense	23230	exon5			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.298C>A	9.37:g.79820908C>A	ENSP00000353422:p.Pro100Thr		79010728	NM_001018037	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.60|13.60	2.284501|2.284501	0.40394|0.40394	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000545365	D;D;D;D|.	0.81908|.	-1.55;-1.55;-1.55;-1.55|.	5.34|5.34	0.434|0.434	0.16539|0.16539	.|.	0.253670|.	0.38111|.	N|.	0.001802|.	T|T	0.61578|0.61578	0.2358|0.2358	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.29212|.	0.076;0.237;0.199;0.199|.	B;B;B;B|.	0.34038|.	0.047;0.174;0.117;0.075|.	T|T	0.58880|0.58880	-0.7558|-0.7558	10|5	0.18276|.	T|.	0.48|.	.|.	11.1012|11.1012	0.48174|0.48174	0.0:0.2624:0.6454:0.0921|0.0:0.2624:0.6454:0.0921	.|.	100;100;100;100|.	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;VP13A_HUMAN;.;.|.	T|Y	100|53	ENSP00000365821:P100T;ENSP00000365823:P100T;ENSP00000353422:P100T;ENSP00000349985:P100T|.	ENSP00000349985:P100T|.	P|S	+|+	1|2	0|0	VPS13A|VPS13A	79010728|79010728	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.980000|0.980000	0.70556|0.70556	2.454000|2.454000	0.44979|0.44979	0.237000|0.237000	0.21200|0.21200	0.650000|0.650000	0.86243|0.86243	CCT|TCC		0.274	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
SPATA31D1	389763	broad.mit.edu	37	9	84609589	84609589	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr9:84609589G>T	ENST00000344803.2	+	4	4251	c.4204G>T	c.(4204-4206)Gct>Tct	p.A1402S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1402					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.A1402S(2)									GACTACTGAAGCTCAGAAAAT	0.473																																					p.A1402S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4204T	9						.						27.0	25.0	26.0					9																	84609589		1863	4107	5970	83799409	SO:0001583	missense	389763	exon4				CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4204G>T	9.37:g.84609589G>T	ENSP00000341988:p.Ala1402Ser		83799409	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580971	0.28180	.	.	ENSG00000214929	ENST00000344803	T	0.18338	2.22	2.96	-0.596	0.11657	.	.	.	.	.	T	0.11495	0.0280	L	0.32530	0.975	0.09310	N	1	P	0.41450	0.75	B	0.38755	0.281	T	0.18555	-1.0333	9	0.62326	D	0.03	-0.0216	5.4864	0.16751	0.5448:0.0:0.4552:0.0	.	1402	Q6ZQQ2	F75D1_HUMAN	S	1402	ENSP00000341988:A1402S	ENSP00000341988:A1402S	A	+	1	0	FAM75D1	83799409	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.049000	0.11924	-0.132000	0.11557	0.563000	0.77884	GCT		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
NUTM2F	54754	broad.mit.edu	37	9	97082793	97082793	+	Missense_Mutation	SNP	C	C	G	rs577940402		TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr9:97082793C>G	ENST00000253262.4	-	5	1085	c.1065G>C	c.(1063-1065)aaG>aaC	p.K355N	NUTM2F_ENST00000335456.7_Missense_Mutation_p.K355N|NUTM2F_ENST00000341207.4_Missense_Mutation_p.K355N	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	355	Pro-rich.							p.K236N(5)									GCAGGTGGGCCTTGGTCTCCG	0.706													.|||	1	0.000199681	0.0	0.0	5008	,	,		14002	0.0		0.0	False		,,,				2504	0.001				p.K355N												.	.	5	Substitution - Missense(5)	large_intestine(5)	c.G1065C	9						.						17.0	24.0	21.0					9																	97082793		1985	4123	6108	96122614	SO:0001583	missense	54754	exon5				CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1065G>C	9.37:g.97082793C>G	ENSP00000253262:p.Lys355Asn		96122614	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	.	10.88	1.475748	0.26511	.	.	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	T;T;T	0.24151	1.87;2.67;2.67	0.1	0.1	0.14510	.	.	.	.	.	T	0.30070	0.0753	N	0.24115	0.695	0.09310	N	1	D	0.57899	0.981	D	0.69824	0.966	T	0.14062	-1.0486	9	0.62326	D	0.03	.	5.97	0.19346	0.0:0.9994:0.0:6.0E-4	.	355	A1L443	FA22F_HUMAN	N	355	ENSP00000335067:K355N;ENSP00000253262:K355N;ENSP00000343865:K355N	ENSP00000253262:K355N	K	-	3	2	FAM22F	96122614	0.001000	0.12720	0.113000	0.21522	0.093000	0.18481	0.349000	0.20055	0.170000	0.19704	0.173000	0.16961	AAG		0.706	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
C5	727	broad.mit.edu	37	9	123744988	123744988	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chr9:123744988T>C	ENST00000223642.1	-	26	3364	c.3335A>G	c.(3334-3336)cAa>cGa	p.Q1112R		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1112					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.Q1112R(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	ATTATCTAATTGATAATTCTC	0.289																																					p.Q1112R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3335G	9						.						62.0	63.0	63.0					9																	123744988		2201	4288	6489	122784809	SO:0001583	missense	727	exon26			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.3335A>G	9.37:g.123744988T>C	ENSP00000223642:p.Gln1112Arg		122784809	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.923251	0.52653	.	.	ENSG00000106804	ENST00000223642	T	0.59083	0.29	5.42	5.42	0.78866	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.000000	0.85682	D	0.000000	T	0.80989	0.4730	H	0.94698	3.57	0.44316	D	0.997195	D	0.52996	0.957	P	0.62298	0.9	D	0.86474	0.1787	10	0.87932	D	0	.	14.6318	0.68660	0.0:0.0:0.0:1.0	.	1112	P01031	CO5_HUMAN	R	1112	ENSP00000223642:Q1112R	ENSP00000223642:Q1112R	Q	-	2	0	C5	122784809	1.000000	0.71417	0.152000	0.22495	0.333000	0.28666	5.110000	0.64622	2.062000	0.61559	0.397000	0.26171	CAA		0.289	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
AMER1	139285	broad.mit.edu	37	X	63411783	63411783	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	C	C	A	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chrX:63411783C>A	ENST00000330258.3	-	2	1656	c.1384G>T	c.(1384-1386)Gaa>Taa	p.E462*	AMER1_ENST00000374869.3_Nonsense_Mutation_p.E462*|AMER1_ENST00000403336.1_Nonsense_Mutation_p.E462*	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	462					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.E462*(2)									GGGGCGGATTCTTGCTGGTCA	0.547																																					p.E462X												.	.	69	Whole gene deletion(67)|Substitution - Nonsense(2)	kidney(65)|large_intestine(3)|ovary(1)	c.G1384T	X						.						95.0	71.0	79.0					X																	63411783		2203	4300	6503	63328508	SO:0001587	stop_gained	139285	exon2			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1384G>T	X.37:g.63411783C>A	ENSP00000329117:p.Glu462*		63328508	NM_152424	A2IB86|Q8N885	Nonsense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	40	8.150724	0.98678	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	.	.	.	5.32	5.32	0.75619	.	0.191892	0.43416	D	0.000580	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.9457	16.762	0.85514	0.0:1.0:0.0:0.0	.	.	.	.	X	462	.	ENSP00000329117:E462X	E	-	1	0	FAM123B	63328508	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	7.320000	0.79064	2.618000	0.88619	0.600000	0.82982	GAA		0.547	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
NAP1L3	4675	broad.mit.edu	37	X	92927638	92927638	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3530-01A-01W-0995-10	TCGA-AA-3530-10A-01W-0995-10	g.chrX:92927638T>A	ENST00000373079.3	-	1	929	c.666A>T	c.(664-666)gaA>gaT	p.E222D	NAP1L3_ENST00000475430.2_Missense_Mutation_p.E215D|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	222	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.E222D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						CTTTAGGAACTTCCTTTTCTT	0.408																																					p.E222D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A666T	X						.						109.0	111.0	110.0					X																	92927638		2203	4300	6503	92814294	SO:0001583	missense	4675	exon1				CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.666A>T	X.37:g.92927638T>A	ENSP00000362171:p.Glu222Asp		92814294	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	T	8.477	0.858831	0.17178	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.27720	1.65	3.44	-2.03	0.07365	.	0.600289	0.13633	N	0.373555	T	0.08670	0.0215	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.27434	-1.0074	10	0.13108	T	0.6	.	0.9797	0.01433	0.174:0.3589:0.1733:0.2938	.	222	Q99457	NP1L3_HUMAN	D	222;215	ENSP00000362171:E222D	ENSP00000362171:E222D	E	-	3	2	NAP1L3	92814294	0.008000	0.16893	0.000000	0.03702	0.434000	0.31775	0.471000	0.22100	-0.519000	0.06444	0.430000	0.28490	GAA		0.408	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
